pygenometracks: pyGenomeTracks.xml annotate

annotate pyGenomeTracks.xml @ 15:c7af51147b55 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068

author	iuc
date	Wed, 01 Oct 2025 19:34:28 +0000
parents	d640aa8a24ab
children

rev	line source
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1 <tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2 <description>plot genomic data tracks</description>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3 <macros>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	4 <token name="@BINARY@">pyGenomeTracks</token>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	5 <import>macros.xml</import>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	6 </macros>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	7 <expand macro="xrefs" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	8 <expand macro="requirements" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	9 <command detect_errors="exit_code">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	10 <![CDATA[
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	11 ## First symlink data
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	12 ## of hic to have the good extension
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	13 ## of fasta to have the index written in the working directory
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	14 #for $counter, $track in enumerate($tracks):
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	15 #if $track.track_file_style_conditional.track_file_style_selector in ["hic_matrix_option", "hic_matrix_square_option"]:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	16 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	17 #set ext = $data_matrix.extension
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	18 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	19 #end for
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	20 #end if
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	21 #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	22 #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	23 ln -s $track.track_file_style_conditional.fasta_source.fasta_local fasta_${counter}.fa &&
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	24 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	25 #end if
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	26 #end for
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	27
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	28
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	29 sed '/^$/d' '$tracks_config' &&
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	30 @BINARY@
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	31 --tracks '$tracks_config'
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	32 --region '$region'
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	33 #if $global_args.title != '':
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	34 --title '$global_args.title'
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	35 #end if
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	36 #if $global_args.plotWidth != '':
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	37 --plotWidth $global_args.plotWidth
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	38 #else:
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	39 --width $global_args.width
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	40 #end if
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	41 #if $global_args.height != '':
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	42 --height '$global_args.height'
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	43 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	44 --fontSize $global_args.fontsize
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	45 --dpi $global_args.dpi
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	46 --trackLabelFraction $global_args.trackLabelFraction
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	47 --trackLabelHAlign $global_args.trackLabelHAlign
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	48 --outFileName plot.$image_file_format
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	49 $global_args.decreasingXAxis
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	50 && mv plot.$image_file_format plot
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	51 ]]>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	52 </command>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	53 <configfiles>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	54 <configfile name="tracks_config">
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	55 ## Each track:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	56 #for $counter, $track in enumerate($tracks):
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	57 ## Hi-C Track triangle
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	58 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	59 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	60 [hic_section_${counter}_${counter_matrix}]
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	61 #set ext = $data_matrix.extension
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	62 file = ${counter}_${counter_matrix}.$ext
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	63 file_type = hic_matrix
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	64 #if $track.track_file_style_conditional.title:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	65 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	66 #else:
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	67 title = $data_matrix.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	68 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	69 #if $track.track_file_style_conditional.depth:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	70 depth = $track.track_file_style_conditional.depth
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	71 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	72 #if $track.track_file_style_conditional.colormap:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	73 colormap = $track.track_file_style_conditional.colormap
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	74 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	75 #if $track.track_file_style_conditional.min_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	76 min_value = $track.track_file_style_conditional.min_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	77 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	78 #if $track.track_file_style_conditional.max_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	79 max_value = $track.track_file_style_conditional.max_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	80 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	81 transform = $track.track_file_style_conditional.transform
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	82 #if $track.track_file_style_conditional.height_matrix != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	83 height = $track.track_file_style_conditional.height_matrix
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	84 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	85 #if $track.track_file_style_conditional.show_masked_bins:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	86 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	87 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	88 #if $track.track_file_style_conditional.invert_orientation:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	89 orientation = inverted
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	90 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	91 #if $track.track_file_style_conditional.scale_factor:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	92 scale_factor = $track.track_file_style_conditional.scale_factor
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	93 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	94 rasterize = $track.track_file_style_conditional.rasterize
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	95 ## If a boundary file is given a new section needs to be written:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	96 #if str($track.track_file_style_conditional.boundaries_file) != "None":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	97 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	98 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	99 #else:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	100 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	101 #end if
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	102 [tads_${counter}_${counter_matrix}]
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	103 file = $boundary_file
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	104 file_type = domains
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	105 border_color = black
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	106 color = none
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	107 overlay_previous = share-y
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	108 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	109 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	110 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	111 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	112 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	113 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	114 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	115 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	116
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	117 ## Hi-C Track square
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	118 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_square_option":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	119 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	120 [hic_section_${counter}_${counter_matrix}]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	121 #set ext = $data_matrix.extension
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	122 file = ${counter}_${counter_matrix}.$ext
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	123 file_type = hic_matrix_square
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	124 #if $track.track_file_style_conditional.title:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	125 title = $track.track_file_style_conditional.title
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	126 #else:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	127 title = $data_matrix.element_identifier
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	128 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	129 #if $track.track_file_style_conditional.region2:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	130 region2 = $track.track_file_style_conditional.region2
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	131 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	132 #if $track.track_file_style_conditional.colormap:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	133 colormap = $track.track_file_style_conditional.colormap
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	134 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	135 #if $track.track_file_style_conditional.min_value != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	136 min_value = $track.track_file_style_conditional.min_value
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	137 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	138 #if $track.track_file_style_conditional.max_value != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	139 max_value = $track.track_file_style_conditional.max_value
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	140 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	141 transform = $track.track_file_style_conditional.transform
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	142 #if $track.track_file_style_conditional.height_matrix != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	143 height = $track.track_file_style_conditional.height_matrix
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	144 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	145 #if $track.track_file_style_conditional.show_masked_bins:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	146 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	147 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	148 #if $track.track_file_style_conditional.invert_orientation:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	149 orientation = inverted
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	150 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	151 #if $track.track_file_style_conditional.scale_factor:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	152 scale_factor = $track.track_file_style_conditional.scale_factor
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	153 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	154 rasterize = $track.track_file_style_conditional.rasterize
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	155 ## If a boundary file is given a new section needs to be written:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	156 #if str($track.track_file_style_conditional.boundaries_file) != "None":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	157 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	158 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	159 #else:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	160 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	161 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	162 [tads_${counter}_${counter_matrix}]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	163 file = $boundary_file
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	164 file_type = bed
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	165 display = squares
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	166 border_color = black
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	167 color = none
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	168 overlay_previous = share-y
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	169 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	170 ## If spacer is asked a new section is created:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	171 #if $track.track_file_style_conditional.spacer_height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	172 [spacer]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	173 height = $track.track_file_style_conditional.spacer_height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	174 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	175 #end for
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	176 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	177
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	178 ## Chrom_state track
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	179 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	180 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	181 [chrom states_$counter]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	182 file = $data_bed
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	183 #if $track.track_file_style_conditional.title:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	184 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	185 #else:
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	186 title = $data_bed.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	187 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	188 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	189 color = bed_rgb
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	190 #elif $track.track_file_style_conditional.color_bed.color:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	191 color = $track.track_file_style_conditional.color_bed.color
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	192 #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap":
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	193 #if str($track.track_file_style_conditional.color_bed.min_value) != '':
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	194 min_value = $track.track_file_style_conditional.color_bed.min_value
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	195 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	196 #if str($track.track_file_style_conditional.color_bed.max_value) != '':
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	197 max_value = $track.track_file_style_conditional.color_bed.max_value
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	198 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	199 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	200 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	201 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	202 border_color = $track.track_file_style_conditional.border_color_bed.color
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	203 #else
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	204 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	205 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	206 display = collapsed
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	207 #if $track.track_file_style_conditional.height_chrom:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	208 height = $track.track_file_style_conditional.height_chrom
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	209 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	210 line_width = $track.track_file_style_conditional.line_width
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	211 file_type = bed
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	212 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	213 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	214 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	215 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	216 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	217 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	218 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	219
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	220 ## Gene/gtf track
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	221 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	222 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.bed_gtf.track_input_bed):
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	223 [genes_${counter}_${counter_bed}]
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	224 file = $data_bed
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	225 #if $track.track_file_style_conditional.bed_gtf.input_bed_or_gtf == "bed":
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	226 file_type = bed
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	227 #else:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	228 file_type = gtf
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	229 prefered_name = $track.track_file_style_conditional.bed_gtf.prefered_name
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	230 #if $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_transcripts_select == 'true':
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	231 merge_transcripts = true
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	232 merge_overlapping_exons = $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_overlapping_exons
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	233 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	234 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	235 #if $track.track_file_style_conditional.title:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	236 title = $track.track_file_style_conditional.title
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	237 #elif $track.track_file_style_conditional.overlay_select == 'no':
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	238 title = $data_bed.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	239 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	240 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	241 color = bed_rgb
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	242 #elif $track.track_file_style_conditional.color_bed.color:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	243 color = $track.track_file_style_conditional.color_bed.color
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	244 #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap":
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	245 #if str($track.track_file_style_conditional.color_bed.min_value) != '':
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	246 min_value = $track.track_file_style_conditional.color_bed.min_value
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	247 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	248 #if str($track.track_file_style_conditional.color_bed.max_value) != '':
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	249 max_value = $track.track_file_style_conditional.color_bed.max_value
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	250 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	251 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	252 #end if
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	253 display = $track.track_file_style_conditional.display_cond.display
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	254 #if $track.track_file_style_conditional.display_cond.display in ['stacked', 'interleaved', 'collapsed']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	255 style = $track.track_file_style_conditional.display_cond.bed_style.bed_style_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	256 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'flybase']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	257 #if $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select == 'manually':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	258 border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	259 #else
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	260 border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	261 #end if
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	262 #end if
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	263 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	264 arrow_interval = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_interval
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	265 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select == "manually":
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	266 color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	267 #else
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	268 color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	269 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	270 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	271 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'UCSC':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	272 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	273 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	274 #else
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	275 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	276 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	277 #else:
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	278 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	279 color_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	280 #elif $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	281 color_utr = bed_rgb
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	282 #else:
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	283 ## This is 'like'
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	284 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	285 color_utr = bed_rgb
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	286 #else:
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	287 color_utr = $track.track_file_style_conditional.color_bed.color
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	288 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	289 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	290 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['flybase', 'tssarrow']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	291 height_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_utr
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	292 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	293 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'exonarrows':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	294 height_intron = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_intron
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	295 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	296 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length != '':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	297 arrow_length = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	298 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	299 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'flybase':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	300 arrowhead_included = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_included
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	301 arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_fraction
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	302 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	303 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	304 #else
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	305 color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	306 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	307 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	308 #end if
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	309 #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'tssarrow']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	310 arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrowhead_fraction
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	311 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	312 #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	313 gene_rows = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	314 #end if
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	315 global_max_row = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.global_max_row
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	316 max_labels = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.max_labels
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	317 line_width = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.line_width
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	318 labels = $track.track_file_style_conditional.display_cond.labels.plot_labels
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	319 #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	320 all_labels_inside = $track.track_file_style_conditional.display_cond.labels.all_labels_inside
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	321 labels_in_margin = $track.track_file_style_conditional.display_cond.labels.labels_in_margin
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	322 fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	323 #if $track.track_file_style_conditional.display_cond.labels.fontsize:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	324 fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	325 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	326 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	327 #end if
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	328 #if $track.track_file_style_conditional.display_cond.display in ['triangle', 'squares']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	329 #if $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select == 'manually':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	330 border_color = $track.track_file_style_conditional.display_cond.border_color_bed.color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	331 #else
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	332 border_color = $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	333 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	334 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	335 #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions', 'triangles', 'squares']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	336 line_width = $track.track_file_style_conditional.display_cond.line_width
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	337 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	338 #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions']:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	339 labels = $track.track_file_style_conditional.display_cond.labels.plot_labels
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	340 #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	341 fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	342 #if $track.track_file_style_conditional.display_cond.labels.fontsize:
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	343 fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	344 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	345 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	346 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	347 #if $track.track_file_style_conditional.display_cond.display == 'deletions':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	348 backbone_color = $track.track_file_style_conditional.display_cond.backbone_color
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	349 #end if
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	350 #if $track.track_file_style_conditional.display_cond.display == 'inversions':
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	351 arrowhead_fraction = $track.track_file_style_conditional.display_cond.arrowhead_fraction
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	352 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	353 #if $track.track_file_style_conditional.height_bed:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	354 height = $track.track_file_style_conditional.height_bed
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	355 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	356 #if $track.track_file_style_conditional.invert_orientation:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	357 orientation = inverted
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	358 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	359 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	360 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	361 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	362 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	363 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	364 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	365 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	366 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	367
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	368 ## Link
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	369 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	370 #for $counter_link, $data_link in enumerate($track.track_file_style_conditional.track_input_link):
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	371 [links_${counter}_${counter_link}]
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	372 file = $data_link
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	373 #if $track.track_file_style_conditional.title:
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	374 title = $track.track_file_style_conditional.title
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	375 #elif $track.track_file_style_conditional.overlay_select == 'no':
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	376 title = $data_link.element_identifier
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	377 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	378 #if $track.track_file_style_conditional.height:
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	379 height = $track.track_file_style_conditional.height
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	380 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	381 #if $track.track_file_style_conditional.min_value != "":
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	382 min_value = $track.track_file_style_conditional.min_value
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	383 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	384 #if $track.track_file_style_conditional.max_value != "":
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	385 max_value = $track.track_file_style_conditional.max_value
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	386 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	387 color = $track.track_file_style_conditional.color_link.color
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	388 alpha = $track.track_file_style_conditional.alpha
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	389 line_width = $track.track_file_style_conditional.line_width
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	390 line_style = $track.track_file_style_conditional.line_style
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	391 links_type = $track.track_file_style_conditional.display.links_type
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	392 #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']:
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	393 compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	394 use_middle = $track.track_file_style_conditional.display.use_middle
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	395 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	396 #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "":
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	397 ylim = $track.track_file_style_conditional.display.ylim
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	398 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	399 #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "":
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	400 region2 = $track.track_file_style_conditional.display.region2
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	401 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	402 #if $track.track_file_style_conditional.invert_orientation:
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	403 orientation = inverted
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	404 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	405 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	406 file_type = links
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	407 ## If spacer is asked a new section is created:
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	408 #if $track.track_file_style_conditional.spacer_height != "":
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	409 [spacer]
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	410 height = $track.track_file_style_conditional.spacer_height
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	411 #end if
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	412 #end for
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	413 #end if
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	414
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	415 ## Narrow peak
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	416 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	417 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	418 [narrow_peak_${counter}_${counter_narrow_peak}]
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	419 file = $data_narrow_peak
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	420 #if $track.track_file_style_conditional.title:
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	421 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	422 #elif $track.track_file_style_conditional.overlay_select == 'no':
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	423 title = $data_narrow_peak.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	424 #end if
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	425 color = $track.track_file_style_conditional.color
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	426 type = $track.track_file_style_conditional.display.display_selector
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	427 use_summit = $track.track_file_style_conditional.display.use_summit
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	428 #if $track.track_file_style_conditional.display.display_selector == "peak":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	429 show_data_range = $track.track_file_style_conditional.display.show_data
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	430 #if $track.track_file_style_conditional.display.width_adjust:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	431 width_adjust = $track.track_file_style_conditional.display.width_adjust
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	432 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	433 #if $track.track_file_style_conditional.display.min_value != "":
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	434 min_value = $track.track_file_style_conditional.display.min_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	435 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	436 #if $track.track_file_style_conditional.display.max_value != "":
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	437 max_value = $track.track_file_style_conditional.display.max_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	438 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	439 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	440 #if $track.track_file_style_conditional.height_narrow_peak:
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	441 height = $track.track_file_style_conditional.height_narrow_peak
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	442 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	443 line_width = $track.track_file_style_conditional.line_width
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	444 file_type = narrow_peak
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	445 show_labels = $track.track_file_style_conditional.labels.show_labels
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	446 #if $track.track_file_style_conditional.labels.show_labels == 'true':
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	447 #if $track.track_file_style_conditional.labels.fontsize:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	448 fontsize = $track.track_file_style_conditional.labels.fontsize
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	449 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	450 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	451 #if $track.track_file_style_conditional.invert_orientation:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	452 orientation = inverted
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	453 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	454 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	455 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	456 #if $track.track_file_style_conditional.spacer_height != "":
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	457 [spacer]
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	458 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	459 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	460 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	461 #end if
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	462
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	463 ## Bedgraph track
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	464 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	465 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	466 [bedgraph_$counter]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	467 file = $data_bedgraph
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	468 #if $track.track_file_style_conditional.title:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	469 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	470 #elif $track.track_file_style_conditional.overlay_select == "no":
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	471 title = $data_bedgraph.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	472 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	473 #if $track.track_file_style_conditional.color:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	474 color = $track.track_file_style_conditional.color
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	475 #end if
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	476 alpha = $track.track_file_style_conditional.alpha
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	477 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	478 negative_color = $track.track_file_style_conditional.color_negative.color
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	479 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	480 #if $track.track_file_style_conditional.height_bedgraph:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	481 height = $track.track_file_style_conditional.height_bedgraph
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	482 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	483 #if $track.track_file_style_conditional.min_value != "":
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	484 min_value = $track.track_file_style_conditional.min_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	485 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	486 #if $track.track_file_style_conditional.max_value != "":
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	487 max_value = $track.track_file_style_conditional.max_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	488 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	489 show_data_range = $track.track_file_style_conditional.show_data
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	490 grid = $track.track_file_style_conditional.grid
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	491 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	492 use_middle = $track.track_file_style_conditional.use_middle
13 e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	493 #if int(data_bedgraph.metadata.columns) > 4:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	494 file_type = bedgraph_matrix
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	495 type = lines
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	496 #else:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	497 file_type = bedgraph
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	498 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	499 type = fill
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	500 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	501 type = line:$track.track_file_style_conditional.type_conditional.width_line
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	502 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	503 type = points:$track.track_file_style_conditional.type_conditional.width_point
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	504 #end if
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	505 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	506 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	507 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	508 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	509 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	510 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	511 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	512 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	513 #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	514 summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	515 #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	516 number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	517 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	518 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	519 #if $track.track_file_style_conditional.op.operation != 'file':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	520 operation = $track.track_file_style_conditional.op.operation
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	521 #if 'second_file' in str($track.track_file_style_conditional.op.operation):
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	522 second_file = $track.track_file_style_conditional.op.second_file
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	523 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	524 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	525 #if $track.track_file_style_conditional.invert_orientation:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	526 orientation = inverted
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	527 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	528 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	529 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	530 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	531 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	532 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	533 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	534 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	535 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	536
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	537 ## Bigwig tracks
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	538 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	539 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	540 [bigwig_$counter]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	541 file = $data_bigwig
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	542 #if $track.track_file_style_conditional.title:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	543 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	544 #elif $track.track_file_style_conditional.overlay_select == "no":
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	545 title = $data_bigwig.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	546 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	547 #if $track.track_file_style_conditional.color:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	548 color = $track.track_file_style_conditional.color
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	549 #end if
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	550 alpha = $track.track_file_style_conditional.alpha
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	551 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	552 negative_color = $track.track_file_style_conditional.color_negative.color
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	553 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	554 #if $track.track_file_style_conditional.min_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	555 min_value = $track.track_file_style_conditional.min_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	556 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	557 #if $track.track_file_style_conditional.max_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	558 max_value = $track.track_file_style_conditional.max_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	559 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	560 height = $track.track_file_style_conditional.height_bigwig
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	561 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	562 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	563 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	564 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	565 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	566 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	567 type = fill
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	568 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	569 type = line:$track.track_file_style_conditional.type_conditional.width_line
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	570 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	571 type = points:$track.track_file_style_conditional.type_conditional.width_point
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	572 #end if
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	573 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	574 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	575 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	576 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	577 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	578 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	579 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	580 #if $track.track_file_style_conditional.op.operation != 'file':
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	581 operation = $track.track_file_style_conditional.op.operation
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	582 #if 'second_file' in $track.track_file_style_conditional.op.operation:
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	583 second_file = $track.track_file_style_conditional.op.second_file
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	584 #end if
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	585 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	586 show_data_range = $track.track_file_style_conditional.show_data
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	587 grid = $track.track_file_style_conditional.grid
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	588 file_type = bigwig
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	589 #if $track.track_file_style_conditional.invert_orientation:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	590 orientation = inverted
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	591 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	592 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	593 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	594 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	595 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	596 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	597 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	598 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	599 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	600
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	601 ## bedgraph_matrix
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	602 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	603 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	604 [bedgraph_matrix_$counter]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	605 file = $data_bedgraph_matrix
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	606 #if $track.track_file_style_conditional.title:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	607 title = $track.track_file_style_conditional.title
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	608 #else:
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	609 title = $data_bedgraph_matrix.element_identifier
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	610 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	611 #if $track.track_file_style_conditional.height_bedgraph:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	612 height = $track.track_file_style_conditional.height_bedgraph
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	613 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	614 #if $track.track_file_style_conditional.min_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	615 min_value = $track.track_file_style_conditional.min_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	616 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	617 #if $track.track_file_style_conditional.max_value != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	618 max_value = $track.track_file_style_conditional.max_value
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	619 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	620 type = $track.track_file_style_conditional.type.type_selector
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	621 file_type = bedgraph_matrix
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	622 #if $track.track_file_style_conditional.type.type_selector == 'lines':
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	623 show_data_range = $track.track_file_style_conditional.type.show_data
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	624 plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	625 pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	626 individual_color = $track.track_file_style_conditional.type.individual_color
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	627 summary_color = $track.track_file_style_conditional.type.summary_color
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	628 #else
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	629 colormap = $track.track_file_style_conditional.type.colormap
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	630 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	631 #if $track.track_file_style_conditional.invert_orientation:
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	632 orientation = inverted
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	633 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	634 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	635 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	636 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	637 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	638 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	639 #end for
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	640 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	641
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	642 ## Vlines:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	643 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	644 [vlines_$counter]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	645 file = $track.track_file_style_conditional.track_input_bed_single
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	646 line_width = $track.track_file_style_conditional.line_width
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	647 line_style = $track.track_file_style_conditional.line_style
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	648 color = $track.track_file_style_conditional.color
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	649 alpha = $track.track_file_style_conditional.alpha
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	650 zorder = $track.track_file_style_conditional.zorder
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	651 type = vlines
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	652 #end if
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	653
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	654 ## Vhighlight:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	655 #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	656 [vhighlight_$counter]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	657 file = $track.track_file_style_conditional.track_input_bed_single
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	658 line_width = $track.track_file_style_conditional.line_width
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	659 color = $track.track_file_style_conditional.color
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	660 alpha = $track.track_file_style_conditional.alpha
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	661 border_color = $track.track_file_style_conditional.border_color
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	662 type = vhighlight
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	663 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	664
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	665 ## Hlines:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	666 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	667 [hlines_$counter]
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	668 #if $track.track_file_style_conditional.title:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	669 title = $track.track_file_style_conditional.title
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	670 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	671 #if $track.track_file_style_conditional.height:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	672 height = $track.track_file_style_conditional.height
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	673 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	674 #if $track.track_file_style_conditional.min_value != "":
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	675 min_value = $track.track_file_style_conditional.min_value
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	676 #end if
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	677 #if $track.track_file_style_conditional.max_value != "":
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	678 max_value = $track.track_file_style_conditional.max_value
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	679 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	680 y_values = $track.track_file_style_conditional.y_values
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	681 show_data_range = $track.track_file_style_conditional.show_data
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	682 color = $track.track_file_style_conditional.color
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	683 alpha = $track.track_file_style_conditional.alpha
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	684 line_width = $track.track_file_style_conditional.line_width
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	685 line_style = $track.track_file_style_conditional.line_style
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	686 #if $track.track_file_style_conditional.invert_orientation:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	687 orientation = inverted
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	688 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	689 overlay_previous = $track.track_file_style_conditional.overlay_select
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	690 file_type = hlines
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	691 ## If spacer is asked a new section is created:
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	692 #if $track.track_file_style_conditional.spacer_height != "":
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	693 [spacer]
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	694 height = $track.track_file_style_conditional.spacer_height
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	695 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	696 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	697
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	698 ## Spacer
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	699 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	700 [spacer]
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	701 #if $track.track_file_style_conditional.title:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	702 title = $track.track_file_style_conditional.title
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	703 #end if
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	704 #if $track.track_file_style_conditional.spacer_height != "":
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	705 height = $track.track_file_style_conditional.spacer_height
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	706 #end if
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	707 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	708
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	709 ## Xaxis:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	710 #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	711 [x-axis]
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	712 #if $track.track_file_style_conditional.title:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	713 title = $track.track_file_style_conditional.title
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	714 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	715 #if $track.track_file_style_conditional.fontsize != "":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	716 fontsize = $track.track_file_style_conditional.fontsize
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	717 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	718 where = $track.track_file_style_conditional.xaxis_where
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	719 ## If spacer is asked a new section is created:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	720 #if $track.track_file_style_conditional.spacer_height != "":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	721 [spacer]
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	722 height = $track.track_file_style_conditional.spacer_height
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	723 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	724 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	725
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	726 ## Scale bar:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	727 #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	728 [scale_bar]
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	729 #if $track.track_file_style_conditional.title:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	730 title = $track.track_file_style_conditional.title
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	731 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	732 #if $track.track_file_style_conditional.color != "":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	733 color = $track.track_file_style_conditional.color
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	734 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	735 alpha = $track.track_file_style_conditional.alpha
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	736 line_width = $track.track_file_style_conditional.line_width
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	737 #if $track.track_file_style_conditional.scalebar_pos.x_center != "":
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	738 x_center = $track.track_file_style_conditional.scalebar_pos.x_center
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	739 #end if
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	740 #if $track.track_file_style_conditional.scalebar_pos.size != "":
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	741 size = $track.track_file_style_conditional.scalebar_pos.size
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	742 #end if
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	743 #if $track.track_file_style_conditional.scalebar_pos.scalebar_start_position != "":
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	744 scalebar_start_position = $track.track_file_style_conditional.scalebar_pos.scalebar_start_position
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	745 #end if
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	746 #if $track.track_file_style_conditional.scalebar_pos.scalebar_end_position != "":
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	747 scalebar_end_position = $track.track_file_style_conditional.scalebar_pos.scalebar_end_position
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	748 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	749 where = $track.track_file_style_conditional.sb_where
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	750 #if $track.track_file_style_conditional.fontsize != "":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	751 fontsize = $track.track_file_style_conditional.fontsize
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	752 #end if
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	753 #if $track.track_file_style_conditional.height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	754 height = $track.track_file_style_conditional.height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	755 #end if
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	756 file_type = scalebar
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	757 ## If spacer is asked a new section is created:
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	758 #if $track.track_file_style_conditional.spacer_height != "":
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	759 [spacer]
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	760 height = $track.track_file_style_conditional.spacer_height
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	761 #end if
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	762 #end if
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	763
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	764 ## Fasta:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	765 #if $track.track_file_style_conditional.track_file_style_selector == "fasta_option":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	766 [Fasta_${counter}]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	767 #if $track.track_file_style_conditional.fasta_source.fasta_source_selector == "history":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	768 file = fasta_${counter}.fa
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	769 #else:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	770 file = $track.track_file_style_conditional.fasta_source.fasta_cached.fields.path
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	771 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	772 #if $track.track_file_style_conditional.title:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	773 title = $track.track_file_style_conditional.title
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	774 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	775 #if $track.track_file_style_conditional.height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	776 height = $track.track_file_style_conditional.height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	777 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	778 #if $track.track_file_style_conditional.invert_orientation:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	779 orientation = inverted
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	780 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	781 overlay_previous = $track.track_file_style_conditional.overlay_select
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	782 file_type = fasta
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	783 ## If spacer is asked a new section is created:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	784 #if $track.track_file_style_conditional.spacer_height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	785 [spacer]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	786 height = $track.track_file_style_conditional.spacer_height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	787 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	788 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	789
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	790 ## Maf:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	791 #if $track.track_file_style_conditional.track_file_style_selector == "maf_option":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	792 [Maf_${counter}]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	793 file = $track.track_file_style_conditional.track_input_maf
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	794 file_index = $track.track_file_style_conditional.track_input_maf.metadata.maf_index
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	795 reference = $track.track_file_style_conditional.reference
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	796 #if $track.track_file_style_conditional.title:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	797 title = $track.track_file_style_conditional.title
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	798 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	799 #if $track.track_file_style_conditional.height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	800 height = $track.track_file_style_conditional.height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	801 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	802 #if $track.track_file_style_conditional.invert_orientation:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	803 orientation = inverted
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	804 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	805 overlay_previous = $track.track_file_style_conditional.overlay_select
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	806 line_width = $track.track_file_style_conditional.line_width
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	807 color_identical = $track.track_file_style_conditional.color_identical
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	808 color_mismatch = $track.track_file_style_conditional.color_mismatch
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	809 color_gap = $track.track_file_style_conditional.color_gap
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	810 #if $track.track_file_style_conditional.species_order != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	811 species_order = $track.track_file_style_conditional.species_order
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	812 #if $track.track_file_style_conditional.species_labels != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	813 species_labels = $track.track_file_style_conditional.species_labels
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	814 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	815 species_order_only = $track.track_file_style_conditional.species_order_only
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	816 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	817 display_ref_seq = $track.track_file_style_conditional.display_ref_seq
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	818 rasterize = $track.track_file_style_conditional.rasterize
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	819 file_type = maf
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	820 ## If spacer is asked a new section is created:
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	821 #if $track.track_file_style_conditional.spacer_height != "":
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	822 [spacer]
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	823 height = $track.track_file_style_conditional.spacer_height
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	824 #end if
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	825 #end if
1 f4b8c2ccc5f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf iuc parents: 0 diff changeset	826 #end for
f4b8c2ccc5f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf iuc parents: 0 diff changeset	827 </configfile>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	828 </configfiles>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	829 <inputs>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	830 <!--Arguments for pgt-->
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	831 <param argument="--region" type="text" label="Region of the genome to plot" optional="false"
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	832 help="The format is chr:start-end, for example chr10:10-500">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	833 <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	834 </param>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	835 <section name="global_args" title="Configure figure parameters" expanded="False">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	836 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	837 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	838 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	839 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	840 <param argument="--width" type="float" label="Figure width in cm" value="40"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	841 <param argument="--plotWidth" type="float" label="Width in centimeters of the plotting (central) part" optional="true"
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	842 help="This will overwrite what has been defined as a figure width."/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	843 <param argument="--height" type="float" label="Figure height in centimeters" optional="true"
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	844 help="If not given, the figure height is computed based on the heights of the tracks. If given, the track height are proportionally scaled to match the desired figure height."/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	845 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	846 min="0" max="1"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	847 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	848 <option value="left" selected="True">left</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	849 <option value="right">right</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	850 <option value="center">center</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	851 </param>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	852 <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false"
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	853 label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	854 </section>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	855 <!--Info to build the config file-->
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	856 <repeat name="tracks" min="1" title="Include tracks in your plot"
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	857 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	858 The order you add them represent the order they will be plotted from top to bottom.">
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	859 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	860 <param name="track_file_style_selector" type="select" label="Choose style of the track">
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	861 <option value="hic_matrix_option">TAD visualization (triangle)</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	862 <option value="hic_matrix_square_option">TAD visualization (square)</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	863 <option value="chrom_states_option">Chromatine states</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	864 <option value="gene_track_option">Gene track / Bed track</option>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	865 <option value="link_track_option">Link track</option>
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	866 <option value="narrow_peak_track_option">NarrowPeak track</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	867 <option value="bigwig_track_option">Bigwig track</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	868 <option value="bedgraph_track_option">Bedgraph track </option>
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	869 <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	870 <option value="vlines_track_option">Vlines track</option>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	871 <option value="vhighlight_track_option">Vhighlight track</option>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	872 <option value="hlines_track_option">Hlines track</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	873 <option value="spacer_option">Spacer</option>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	874 <option value="xaxis_option">X-axis</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	875 <option value="scale_bar_option">Scale bar track</option>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	876 <option value="fasta_option">Fasta track</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	877 <option value="maf_option">Maf track</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	878 </param>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	879 <when value="hic_matrix_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	880 <expand macro="plot_title" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	881 <expand macro="matrix_h5_cooler_multiple_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	882
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	883 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	884 <option value="RdYlBu_r">RdYlBu reversed</option>
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	885 <option value="viridis">viridis</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	886 <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	887 </param>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	888 <expand macro="minmax_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	889 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	890 <param name="transform" type="select" label="Plot the transformed value">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	891 <option value="log1p" selected="True" >log1p</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	892 <option value="log">log</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	893 <option value="-log">-log</option>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	894 <option value="no">no transformation</option>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	895
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	896 </param>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	897 <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares rotated 45 degrees."/>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	898 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	899 label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	900 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display triangles on top of the heatmap"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	901 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	902 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	903 label="Rasterize the heatmap" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	904 <expand macro="inverted_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	905 <expand macro="spacer_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	906
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	907 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	908
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	909 <when value="hic_matrix_square_option">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	910 <expand macro="plot_title" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	911 <expand macro="matrix_h5_cooler_multiple_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	912
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	913 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	914 <option value="RdYlBu_r">RdYlBu reversed</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	915 <option value="viridis">viridis</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	916 <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	917 </param>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	918 <expand macro="minmax_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	919 <expand macro="region2_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	920 <param name="transform" type="select" label="Plot the transformed value">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	921 <option value="log1p" selected="True" >log1p</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	922 <option value="log">log</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	923 <option value="-log">-log</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	924 <option value="no">no transformation</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	925
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	926 </param>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	927 <param name="height_matrix" type="float" value="" optional="True" label="height of the heatmap" help="If you leave it empty the height is calculated to have perfect squares."/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	928 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	929 label="Show masked bins" help="If false, neighbour bins will be increase in size to hide the mask bins." />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	930 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True" help="Will display squares on top of the heatmap"/>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	931 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	932 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	933 label="Rasterize the heatmap" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	934 <expand macro="inverted_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	935 <expand macro="spacer_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	936
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	937 </when>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	938 <when value="chrom_states_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	939 <expand macro="plot_title" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	940 <expand macro="track_input_bed_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	941 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	942 <param name="color_bed_select" type="select" label="Define color:">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	943 <option value="manually" selected="True">manually</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	944 <option value="bed_rgb">From the 9th field</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	945 <option value="colormap">From the 5th field (score)</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	946 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	947 <when value="manually">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	948 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	949 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	950 <when value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	951 <when value="colormap">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	952 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	953 <option value="RdYlBu_r">RdYlBu reversed</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	954 <option value="viridis">viridis</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	955 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	956 </param>
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	957 <expand macro="minmax_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	958 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	959 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	960 <expand macro="border_color_bed_macro" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	961 <param name="line_width" type="float" value="0.5" label="width of lines" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	962 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	963 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	964 label="Plot labels" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	965 <expand macro="spacer_macro" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	966
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	967 </when>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	968 <when value="gene_track_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	969 <expand macro="plot_title" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	970 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	971 <param name="input_bed_or_gtf" type="select" label="Use bed or gtf input:">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	972 <option value="bed" selected="True">bed</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	973 <option value="gtf">gtf</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	974 </param>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	975 <when value="bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	976 <expand macro="track_input_bed_macro" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	977 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	978 <when value="gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	979 <!-- I call it track_input_bed to make it the same name as the bed input -->
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	980 <param name="track_input_bed" type="data" format="gtf" label="Track file(s) gtf format" multiple="True"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	981 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	982 help="Usually transcript_name or gene_name"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	983 <conditional name="merge_transcripts">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	984 <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	985 <option value="false" selected="True">No</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	986 <option value="true">Yes</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	987 </param>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	988 <when value="true">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	989 <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	990 label="Merge overlapping exons" help="Usually it makes prettier plots" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	991 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	992 <when value="false" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	993 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	994 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	995 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	996 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	997 <param name="color_bed_select" type="select" label="Define color:">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	998 <option value="manually" selected="True">manually</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	999 <option value="bed_rgb">From the 9th field</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1000 <option value="colormap">From the 5th field (score)</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1001 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1002 <when value="manually">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1003 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1004 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1005 <when value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1006 <when value="colormap">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1007 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1008 <option value="RdYlBu_r">RdYlBu reversed</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1009 <option value="viridis">viridis</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1010 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1011 </param>
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	1012 <expand macro="minmax_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1013 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1014 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1015 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1016 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1017 <param name="display" type="select" label="display to use">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1018 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1019 <option value="interleaved">interleaved (everything on 2 lines)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1020 <option value="collapsed">collapsed (everything on 1 line)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1021 <option value="triangles">triangles (plot triangles between start and end)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1022 <option value="squares">squares (plot squares on the diagonal)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1023 <option value="deletions">deletions (plot a horizontal line with V for each region of your bed)</option>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1024 <option value="inversions">inversions (plot arrows around each region of your bed)</option>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1025 </param>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1026 <when value="stacked">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1027 <expand macro="bed_style_macro" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1028 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1029 <when value="interleaved">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1030 <expand macro="bed_style_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1031 </when>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1032 <when value="collapsed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1033 <expand macro="bed_style_macro" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1034 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1035 <when value="triangles">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1036 <expand macro="border_color_bed_macro" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1037 <param name="line_width" type="float" value="0.5" label="width of lines" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1038 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1039 <when value="squares">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1040 <expand macro="border_color_bed_macro" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1041 <param name="line_width" type="float" value="0.5" label="width of lines" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1042 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1043 <when value="deletions">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1044 <param name="line_width" type="float" value="0.5" label="width of lines" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1045 <param name="backbone_color" type="color" value="#000000" label="Color of the horizontal line"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1046 <expand macro="delinv_labels"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1047 </when>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1048 <when value="inversions">
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1049 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1050 label="Parameter to control the size of the arrows"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1051 <param name="line_width" type="float" value="0.5" label="width of lines" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1052 <expand macro="delinv_labels"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1053 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1054 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1055 <expand macro="overlay_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1056 <expand macro="inverted_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1057 <expand macro="spacer_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1058 </when>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1059 <when value="link_track_option">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1060 <expand macro="plot_title" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1061 <expand macro="track_input_link_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1062 <conditional name="color_link">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1063 <param name="color_link_select" type="select" label="Define color:">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1064 <option value="manually" selected="True">manually</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1065 <option value="colormap">From the 7th field (score)</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1066 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1067 <when value="manually">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1068 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1069 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1070 <when value="colormap">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1071 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1072 <option value="RdYlBu_r">RdYlBu reversed</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1073 <option value="viridis">viridis</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1074 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1075 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1076 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1077 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1078 <expand macro="lines_macro" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1079 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1080 <param name="links_type" type="select" label="Representation of the link:">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1081 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1082 <option value="triangles">triangles</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1083 <option value="loops">loops (a diamond highlighting the intersection)</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1084 <option value="squares">squares (a square highlighting the intersection symetrically to the diagonal)</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1085 </param>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1086 <when value="arcs">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1087 <expand macro="links_arcs_triangles_options" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1088 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1089 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1090 <when value="triangles">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1091 <expand macro="links_arcs_triangles_options" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1092 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1093 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1094 <when value="loops">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1095 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1096 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1097 <when value="squares">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1098 <expand macro="region2_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1099 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1100 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1101 <param name="height" type="float" value="1.5" optional="True" label="height"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1102 <expand macro="minmax_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1103 <expand macro="overlay_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1104 <expand macro="inverted_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1105 <expand macro="spacer_macro" />
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	1106 </when>
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1107 <when value="narrow_peak_track_option">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1108 <expand macro="plot_title" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1109 <expand macro="track_input_narrow_peak_macro" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1110 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1111 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1112 <conditional name="display">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1113 <param name="display_selector" type="select" label="display to use">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1114 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1115 <option value="box">box: Draw a box</option>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1116 </param>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1117 <when value="peak">
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1118 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1119 optional="True" label="Use summit information to make the curve." />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1120 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1121 label="Show visualization of data range" />
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	1122 <param name="width_adjust" type="float" value="1.5" optional="True"
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1123 label="Factor to change the width of the curve."/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1124 <expand macro="minmax_macro" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1125 </when>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1126 <when value="box">
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1127 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1128 optional="True" label="Plot a vertical bar at the summit position." />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1129 </when>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1130 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1131 <param name="line_width" type="float" value="1" label="width of lines" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1132 <conditional name="labels">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1133 <param name="show_labels" type="select" label="Plot labels (name, p-val, q-val)">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1134 <option value="true" selected="True">yes</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1135 <option value="false">no</option>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1136 </param>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1137 <when value="true">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1138 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1139 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1140 <when value="false"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1141 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1142 <expand macro="overlay_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1143 <expand macro="inverted_macro" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1144 <expand macro="spacer_macro" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1145
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1146 </when>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1147 <when value="bedgraph_track_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1148 <expand macro="plot_title" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1149 <expand macro="track_input_bedgraph_macro" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1150 <expand macro="color_coverage_macro" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1151 <expand macro="minmax_macro" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1152 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1153 <expand macro="type_coverage_macro" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1154 <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1155 <param name="summary_method" type="select" label="Summary method">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1156 <option value="no" selected="True">no=no summary method (keep all values)</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1157 <option value="mean">mean=mean value</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1158 <option value="min">min=minimum value</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1159 <option value="max">max=maximum value</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1160 <option value="coverage">coverage=number of covered bases</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1161 <option value="std">std=standard deviation</option>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1162 </param>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1163 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1164 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1165 <expand macro="logScale_coverage_macro" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1166 <section name ="op" title="Compute an operation on the file" expanded="False">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1167 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1168 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1169 <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1170 </section>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1171 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1172 label="NAN's to zeros" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1173 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1174 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1175 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1176 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1177 <expand macro="inverted_macro" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1178 <expand macro="overlay_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1179 <expand macro="spacer_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1180 </when>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1181 <when value="bigwig_track_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1182 <expand macro="plot_title" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1183
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1184 <expand macro="track_input_bigwig_macro" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1185 <expand macro="color_coverage_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1186
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1187 <expand macro="minmax_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1188
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1189 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1190 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1191 <param name="summary_method" type="select" label="Summary method">
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1192 <option value="mean" selected="True">mean=mean value</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1193 <option value="min">min=minimum value</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1194 <option value="max">max=maximum value</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1195 <option value="coverage">coverage=number of covered bases</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1196 <option value="std">std=standard deviation</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1197 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1198 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1199 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1200 label="NAN's to zeros" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1201 </section>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1202 <expand macro="type_coverage_macro" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1203 <expand macro="logScale_coverage_macro" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1204 <section name ="op" title="Compute an operation on the file" expanded="False">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1205 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1206 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1207 <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1208 </section>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1209 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1210 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1211 <expand macro="inverted_macro" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1212 <expand macro="overlay_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1213 <expand macro="spacer_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1214
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1215 </when>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1216
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1217 <when value="bedgraph_matrix_track_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1218 <expand macro="plot_title" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1219
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1220 <expand macro="track_input_bedgraph_matrix_macro" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1221 <expand macro="minmax_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1222
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1223 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1224
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1225 <conditional name="type">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1226 <param name="type_selector" type="select" label="type of plotting">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1227 <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1228 <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1229 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1230 <when value="lines">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1231 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1232 label="Plot an horizontal line at 0 when type is lines" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1233 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1234 label="Show visualization of data range" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1235 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1236 <option value="center" selected="True">Center</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1237 <option value="block">Block (draw a horizontal line between start and end)</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1238 </param>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1239 <param name="individual_color" type="color" value="grey" label="Color of the individual lines" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1240 <param name="summary_color" type="color" value="#1f77b4" label="Color of the summary line" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1241 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1242 <when value="matrix">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1243 <param name="colormap" type="select" label="colormap">
10 5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1244 <option value="viridis">viridis</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1245 <option value="RdYlBu_r">RdYlBu reversed</option>
5f9a41f84844 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7" iuc parents: 9 diff changeset	1246 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1247 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1248 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1249 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1250
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1251
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1252 <expand macro="inverted_macro" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1253 <expand macro="spacer_macro" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1254
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1255 </when>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1256 <when value="vlines_track_option">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1257 <expand macro="track_input_bed_single_macro" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1258 <param name="line_width" type="float" value="0.5" label="width of lines"/>
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1259 <param name="line_style" type="select" label="Line Style">
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1260 <option value="dashed">Dashed</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1261 <option value="solid">Solid</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1262 <option value="dotted">Dotted</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1263 <option value="dashdot">Dashdot</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1264 </param>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1265 <param name="color" type="color" value="black" label="color of the vline"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1266 <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1267 <param name="zorder" type="select" label="Plot the vline above or behind other tracks">
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1268 <option value="100">above</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1269 <option value="-100">behind</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1270 </param>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1271 </when>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1272 <when value="vhighlight_track_option">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1273 <expand macro="track_input_bed_single_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1274 <param name="color" type="color" value="yellow" label="color of the highlight"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1275 <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/>
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1276 <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" />
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1277 <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1278 <param name="zorder" type="select" label="Plot the highlight above or behind other tracks">
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1279 <option value="-100">behind</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1280 <option value="100">above</option>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	1281 </param>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1282 </when>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1283 <when value="hlines_track_option">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1284 <expand macro="plot_title" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1285 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1286 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1287 <expand macro="lines_macro" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1288 <param name="height" type="float" value="1.5" optional="True" label="height of the Hlines track"/>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1289 <expand macro="minmax_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1290 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1291 <expand macro="inverted_macro" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1292 <expand macro="overlay_macro" />
6 ad2e499da28f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	1293 <expand macro="spacer_macro" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1294 </when>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1295 <when value="spacer_option">
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1296 <expand macro="plot_title" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1297 <param name="spacer_height" type="float" value="" optional="True"
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1298 label="Height of the spacer."/>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1299 </when>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1300 <when value="xaxis_option">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1301 <expand macro="plot_title" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1302 <param name="fontsize" type="float" optional="True"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1303 label="Fontsize of the x-axis."/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1304 <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1305 <option value="bottom" selected="True">below</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1306 <option value="top">above</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1307 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1308 <expand macro="spacer_macro" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1309 </when>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1310 <when value="scale_bar_option">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1311 <expand macro="plot_title" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1312 <param name="color" type="color" label="Color of the scale bar" optional="True" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1313 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1314 <param name="line_width" type="float" value="0.5" label="width of lines"/>
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1315 <section name="scalebar_pos" title="Set the scalebar position" expanded="true" help="You can optionally define one or multiple parameters below.">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1316 <param name="scalebar_start_position" type="integer" label="coordinate where the scale bar should begin." optional="True"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1317 <param name="scalebar_end_position" type="integer" label="coordinate where the scale bar should end." optional="True"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1318 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1319 help="If not set and cannot be deduced from others it will be in the middle of the plotted area."/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1320 <param name="size" type="integer" label="size of the scale bar" optional="True"
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1321 help="If not set and cannot be deduced from others it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	1322 </section>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1323 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1324 <option value="left" selected="True">left</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1325 <option value="right">right</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1326 <option value="bottom">below</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1327 <option value="top">above</option>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1328 </param>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1329 <param name="fontsize" type="float" optional="True"
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1330 label="Fontsize of the size of the scale bar."/>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1331 <param name="height" type="float" value="0.5" optional="True" label="height of the Scale bar track"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1332 <expand macro="spacer_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1333 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1334 <when value="fasta_option">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1335 <expand macro="track_input_fasta_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1336 <expand macro="plot_title" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1337 <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1338 <expand macro="inverted_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1339 <expand macro="overlay_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1340 <expand macro="spacer_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1341 </when>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1342 <when value="maf_option">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1343 <expand macro="track_input_maf_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1344 <expand macro="plot_title" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1345 <param name="height" type="float" value="0.5" optional="True" label="height of the Fasta track"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1346 <param name="reference" type="select" label="Reference">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1347 <options>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1348 <filter type="data_meta" ref="track_input_maf" key="species" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1349 </options>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1350 </param>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1351 <param name="line_width" type="float" value="0.5" label="width of lines"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1352 <param name="color_identical" type="color" label="Color when bases are identical" value="black" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1353 <param name="color_mismatch" type="color" label="Color when bases are different" value="grey" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1354 <param name="color_gap" type="color" label="Color when bases corresponds to gap" value="lightgrey" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1355 <param name="species_order" type="text" value="" label="[Optional] The order you want your species (space separated)"
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1356 help="checkout the choices for reference to see available species"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1357 <param name="species_labels" type="text" value="" label="[Optional] The label you want for the above species (space separated)"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1358 <param name="species_order_only" type="boolean" truevalue="true" falsevalue="false" checked="false"
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1359 label="Display only the species specified above"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1360 <param name="display_ref_seq" type="boolean" truevalue="true" falsevalue="false" checked="false"
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1361 label="Display the sequence of the reference"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1362 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="false"
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1363 label="Rasterize the line and blocks of the maf track"/>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1364 <expand macro="inverted_macro" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1365 <expand macro="overlay_macro" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1366 <expand macro="spacer_macro" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1367 </when>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1368 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1369 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1370 <param name="image_file_format" type="select" label="Image output format">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1371 <option value="png">png</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1372 <option value="svg">svg</option>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1373 </param>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1374 </inputs>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1375 <outputs>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1376 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1377 <change_format>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1378 <when input="image_file_format" value="png" format="png" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1379 <when input="image_file_format" value="svg" format="svg" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1380 </change_format>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1381 </data>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1382 </outputs>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1383 <tests>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1384 <!--test 1-->
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1385 <test>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1386 <param name="region" value="chrX:3000000-3500000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1387 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1388 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1389 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1390 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1391 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1392 </repeat>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1393 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1394 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1395 <param name="track_file_style_selector" value="hic_matrix_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1396 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1397 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1398 <!--<param name="colormap" value="RdYlBu_r" />-->
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1399 <param name="depth" value="200000" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1400 <param name="transform" value="log1p" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1401 <param name="boundaries_file" value="domains.bed" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1402 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1403 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1404 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1405 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1406 <param name="track_file_style_selector" value="spacer_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1407 <param name="spacer_height" value="0.05" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1408 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1409 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1410 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1411 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1412 <param name="track_file_style_selector" value="chrom_states_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1413 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1414 <param name="title" value="TAD state" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1415 <param name="height_chrom" value="0.5" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1416 <param name="labels" value="false" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1417 <conditional name="color_bed">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1418 <param name="color_bed_select" value="bed_rgb" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1419 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1420 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1421 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1422 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1423 <conditional name="track_file_style_conditional">
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1424 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1425 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1426 <param name="title" value="TAD separation score (Ramirez et al.)" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1427 <conditional name="type">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1428 <param name="type_selector" value="matrix" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1429 <!--<param name="colormap" value="viridis" />-->
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1430 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1431 <param name="height_bedgraph" value="10" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1432 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1433 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1434 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1435 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1436 <param name="track_file_style_selector" value="spacer_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1437 <param name="spacer_height" value="1" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1438 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1439 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1440 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1441 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1442 <param name="track_file_style_selector" value="bedgraph_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1443 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1444 <param name="title" value="bedgraph" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1445 <param name="height_bedgraph" value="4" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1446 <param name="color" value="blue" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1447 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1448 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1449 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1450 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1451 <param name="track_file_style_selector" value="bigwig_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1452 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1453 <param name="title" value="rep 1 test fill" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1454 <param name="height_bigwig" value="4" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1455 <param name="color" value="blue" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1456 <conditional name="type_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1457 <param name="type_selector" value="fill_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1458 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1459 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1460 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1461 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1462 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1463 <param name="track_file_style_selector" value="bigwig_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1464 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1465 <param name="title" value="rep 1 test line" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1466 <param name="height_bigwig" value="4" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1467 <param name="color" value="red" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1468 <conditional name="type_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1469 <param name="type_selector" value="line_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1470 <param name="width_line" value="1" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1471 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1472 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1473 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1474 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1475 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1476 <param name="track_file_style_selector" value="bigwig_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1477 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1478 <param name="title" value="rep 1 test lw=0.2" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1479 <param name="height_bigwig" value="4" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1480 <param name="color" value="red" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1481 <conditional name="type_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1482 <param name="type_selector" value="line_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1483 <param name="width_line" value="0.1" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1484
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1485 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1486 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1487 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1488 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1489 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1490 <param name="track_file_style_selector" value="bigwig_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1491 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1492 <param name="title" value="rep 1 test point:0.5" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1493 <param name="height_bigwig" value="4" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1494 <param name="color" value="black" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1495 <conditional name="type_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1496 <param name="type_selector" value="point_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1497 <param name="width_point" value="0.5" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1498
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1499 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1500 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1501 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1502 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1503 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1504 <param name="track_file_style_selector" value="spacer_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1505 <param name="spacer_height" value="0.5" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1506 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1507 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1508 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1509 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1510 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1511 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1512 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1513 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1514 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1515 <param name="title" value="genes" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1516 <param name="height_bed" value="5" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1517 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1518 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1519 <param name="fontsize" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1520 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	1521 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1522 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1523 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1524 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1525 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1526 <param name="track_file_style_selector" value="spacer_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1527 <param name="spacer_height" value="1" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1528 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1529 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1530 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1531 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1532 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1533 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1534 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1535 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1536 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1537 <param name="title" value="max num rows 3" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1538 <param name="height_bed" value="3" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1539 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1540 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1541 <param name="fontsize" value="8" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1542 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1543 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1544 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1545 <param name="gene_rows" value="3" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1546 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1547 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1548 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1549 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1550 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1551 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1552 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1553 <param name="track_file_style_selector" value="spacer_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1554 <param name="spacer_height" value="1" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1555 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1556 </repeat>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1557 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1558 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1559 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1560 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1561 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1562 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1563 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1564 <param name="title" value="bed6 global max row" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1565 <param name="height_bed" value="20" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1566 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1567 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1568 <param name="fontsize" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1569 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1570 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1571 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1572 <param name="global_max_row" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1573 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1574 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1575 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1576 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1577 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1578 <repeat name="tracks">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1579 <conditional name="track_file_style_conditional">
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1580 <param name="track_file_style_selector" value="vlines_track_option" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1581 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1582 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1583 </repeat>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1584 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1585 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="image_diff" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1586 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1587 <!--test 2-->
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1588 <test>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1589 <param name="region" value="chrX:3000000-3500000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1590 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1591 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1592 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1593 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1594 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1595 </repeat>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1596 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1597 <conditional name="track_file_style_conditional">
13 e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1598 <param name="track_file_style_selector" value="bedgraph_track_option" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1599 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg,bedgraph2_X_2.5e6_3.5e6.bdg,tad_score.gz" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1600 <param name="title" value="rep bed" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1601 <param name="show_data" value="true" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1602 <conditional name="type_conditional">
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1603 <param name="type_selector" value="point_option" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1604 <param name="width_point" value="2" />
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1605 </conditional>
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1606 </conditional>
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1607 </repeat>
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1608 <repeat name="tracks">
e0c00f68067f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b7df28a308484a4af1d33e0ddc2c4e391643ec1e iuc parents: 12 diff changeset	1609 <conditional name="track_file_style_conditional">
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1610 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1611 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1612 <param name="title" value="rep 1 test line" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1613 <param name="height_bigwig" value="4" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1614 <param name="color" value="red" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1615 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1616 <param name="type_selector" value="line_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1617 <param name="width_line" value="1" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1618 </conditional>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1619 </conditional>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1620 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1621 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1622 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1623 <param name="track_file_style_selector" value="bigwig_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1624 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1625 <param name="title" value="nans_to_zeros" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1626 <param name="height_bigwig" value="4" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1627 <param name="color" value="blue" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1628 <section name="reading_bw_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1629 <param name="nans_to_zeros" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1630 </section>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1631 <param name="show_data" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1632 <conditional name="type_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1633 <param name="type_selector" value="line_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1634 <param name="width_line" value="1" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1635 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1636 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1637 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1638 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1639 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1640 <param name="track_file_style_selector" value="hlines_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1641 <param name="title" value="" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1642 <param name="color" value="orange" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1643 <param name="y_values" value="50" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1644 <param name="line_width" value="2" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1645 <param name="line_style" value="dashed" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1646 <param name="overlay_select" value="share-y" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1647 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1648 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1649 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1650 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1651 <param name="track_file_style_selector" value="hlines_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1652 <param name="title" value="hlines" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1653 <param name="color" value="purple" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1654 <param name="y_values" value="0, 10, 20, 100" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1655 <param name="min_value" value="12" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1656 <param name="show_data" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1657 <param name="invert_orientation" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1658 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1659 </repeat>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1660 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1661 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="image_diff" />
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1662 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1663 <!--test 3-->
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1664 <test>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1665 <param name="region" value="chrX:3000000-3500000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1666 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1667 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1668 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1669 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1670 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1671 </repeat>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1672 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1673 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1674 <param name="track_file_style_selector" value="hic_matrix_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1675 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1676 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1677 <param name="colormap" value="RdYlBu_r" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1678 <param name="depth" value="200000" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1679 <param name="transform" value="log1p" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1680 <param name="boundaries_file" value="domains.bed" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1681 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1682 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1683 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1684 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1685 <param name="track_file_style_selector" value="chrom_states_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1686 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1687 <param name="title" value="TAD state" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1688 <param name="height_chrom" value="0.5" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1689 <param name="labels" value="false" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1690 <conditional name="color_bed">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1691 <param name="color_bed_select" value="bed_rgb" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1692 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1693 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1694 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1695 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1696 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1697 <param name="track_file_style_selector" value="hic_matrix_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1698 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1699 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1700 <param name="colormap" value="Reds" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1701 <param name="depth" value="200000" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1702 <param name="transform" value="no" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1703 <param name="invert_orientation" value="true" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1704 <param name="min_value" value="5" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1705 <param name="max_value" value="70" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1706 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1707 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1708 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1709 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1710 <param name="track_file_style_selector" value="spacer_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1711 <param name="spacer_height" value="1" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1712 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1713 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1714 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1715 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1716 <param name="track_file_style_selector" value="bedgraph_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1717 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1718 <param name="title" value="bedgraph with negative values" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1719 <param name="height_bedgraph" value="4" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1720 <param name="color" value="black" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1721 <conditional name="color_negative">
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1722 <param name="color_negative_select" value="true" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1723 <param name="color" value="red" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1724 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1725 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1726 <param name="type_selector" value="fill_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1727 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1728 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1729 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1730 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1731 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1732 <param name="track_file_style_selector" value="bedgraph_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1733 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1734 <param name="title" value="bedgraph" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1735 <param name="height_bedgraph" value="4" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1736 <param name="color" value="blue" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1737 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1738 <param name="type_selector" value="fill_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1739 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1740 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1741 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1742 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1743 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1744 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1745 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1746 <param name="title" value="rep 1 test fill" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1747 <param name="height_bigwig" value="4" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1748 <param name="color" value="blue" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1749 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1750 <param name="type_selector" value="fill_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1751 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1752 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1753 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1754 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1755 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1756 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1757 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1758 <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1759 <param name="height_bigwig" value="10" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1760 <param name="color" value="red" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1761 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1762 <param name="type_selector" value="point_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1763 <param name="width_point" value="5" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1764 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1765 <section name="reading_bw_conditional">
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1766 <param name="summary_method" value="max"/>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1767 <param name="number_of_bins" value="100"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1768 </section>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1769 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1770 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1771 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1772 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1773 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1774 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1775 <param name="height_bigwig" value="10" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1776 <param name="color" value="#c00000" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1777 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1778 <param name="type_selector" value="line_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1779 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1780 <section name="reading_bw_conditional">
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1781 <param name="summary_method" value="min"/>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1782 </section>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1783 <param name="overlay_select" value="share-y" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1784 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1785 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1786 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1787 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1788 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1789 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1790 <param name="height_bigwig" value="10" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1791 <param name="color" value="black" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1792 <conditional name="type_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1793 <param name="type_selector" value="line_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1794 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1795 <section name="reading_bw_conditional">
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1796 <param name="summary_method" value="min"/>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1797 <param name="number_of_bins" value="30000"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1798 </section>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1799 <param name="overlay_select" value="share-y" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1800 <param name="spacer_height" value="1" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1801 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1802 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1803 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1804 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1805 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1806 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1807 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1808 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1809 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1810 <param name="title" value="genes in ucsc" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1811 <param name="height_bed" value="5" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1812 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1813 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1814 <param name="fontsize" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1815 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1816 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1817 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1818 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1819 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1820 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1821 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1822 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1823 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1824 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1825 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1826 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1827 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1828 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1829 <param name="title" value="bed6 global max row color from score" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1830 <param name="height_bed" value="20" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1831 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1832 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1833 <param name="fontsize" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1834 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1835 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1836 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1837 <param name="global_max_row" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1838 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1839 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1840 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1841 <conditional name="color_bed">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1842 <param name="color_bed_select" value="colormap" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1843 <param name="color" value="RdYlBu_r" />
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	1844 <param name="min_value" value="0" />
d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	1845 <param name="max_value" value="2" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1846 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1847 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1848 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1849 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1850 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1851 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1852 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1853 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1854 <param name="track_input_bed" value="domains.bed" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1855 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1856 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1857 <param name="height_bed" value="2" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1858 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1859 <param name="color_bed_select" value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1860 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1861 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1862 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1863 <conditional name="border_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1864 <param name="border_color_bed_select" value="manually" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1865 <param name="color" value="red" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1866 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1867 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1868 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1869 <param name="plot_labels" value="false" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1870 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1871 <param name="display" value="interleaved" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1872 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1873 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1874 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1875 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1876 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1877 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1878 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1879 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1880 <param name="track_input_bed" value="domains.bed" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1881 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1882 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1883 <param name="height_bed" value="2" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1884 <conditional name="color_bed">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1885 <param name="color_bed_select" value="bed_rgb" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1886 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1887 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1888 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1889 <conditional name="border_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1890 <param name="border_color_bed_select" value="bed_rgb" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1891 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1892 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1893 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1894 <param name="plot_labels" value="false" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1895 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1896 <param name="display" value="interleaved" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1897 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1898 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1899 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1900 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1901 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1902 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1903 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1904 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1905 <param name="track_input_bed" value="domains.bed" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1906 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1907 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1908 <param name="height_bed" value="2" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1909 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1910 <param name="color_bed_select" value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1911 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1912 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1913 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1914 <conditional name="border_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1915 <param name="border_color_bed_select" value="none" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1916 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1917 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1918 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1919 <param name="plot_labels" value="false" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1920 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1921 <param name="display" value="interleaved" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1922 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1923 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1924 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1925 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1926 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="image_diff" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1927 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1928 <!--test 4-->
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1929 <test>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1930 <param name="region" value="X:2700000-3100000"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1931 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1932 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1933 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1934 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1935 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1936 <param name="height_bigwig" value="7" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1937 <param name="color" value="#00b0f0" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1938 <section name="reading_bw_conditional">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1939 <param name="number_of_bins" value="2000"/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1940 </section>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1941 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1942 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1943 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1944 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1945 <param name="track_file_style_selector" value="bigwig_track_option" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1946 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1947 <param name="title" value="" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1948 <param name="color" value="#ff0000" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1949 <param name="alpha" value="0.5" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1950 <section name="reading_bw_conditional">
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1951 <param name="summary_method" value="max" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1952 <param name="number_of_bins" value="300"/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1953 </section>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1954 <param name="overlay_select" value="share-y"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1955 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1956 </repeat>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1957 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1958 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1959 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1960 <param name="xaxis_where" value="bottom" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1961 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1962 </repeat>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1963 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1964 <output name="outFileName" file="test_alpha.png" ftype="png" compare="image_diff" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1965 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1966 <!--test 5-->
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1967 <test>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1968 <param name="region" value="X:3000000-3300000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1969 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1970 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1971 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1972 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1973 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1974 </repeat>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1975 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1976 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1977 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1978 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1979 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1980 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1981 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1982 <param name="title" value="test" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1983 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1984 <conditional name="color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1985 <param name="color" value="#000000" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1986 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1987 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1988 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1989 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1990 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1991 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1992 <param name="spacer_height" value="1"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1993 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1994 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1995 <repeat name="tracks">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1996 <conditional name="track_file_style_conditional">
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1997 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1998 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	1999 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2000 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2001 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2002 <param name="title" value="test" />
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2003 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2004 <conditional name="color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2005 <param name="color" value="#000000" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2006 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2007 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2008 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2009 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2010 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2011 </conditional>
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2012 <param name="spacer_height" value="1"/>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2013 </conditional>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2014 </repeat>
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2015 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2016 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="image_diff" />
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2017 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2018 <!--test 6-->
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2019 <test>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2020 <param name="region" value="X:2760000-2802000"/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2021 <repeat name="tracks">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2022 <conditional name="track_file_style_conditional">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2023 <param name="track_file_style_selector" value="narrow_peak_track_option" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2024 <param name="title" value="box" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2025 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2026 <param name="color" value="#9bbb59" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2027 <param name="height_narrow_peak" value="4" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2028 <conditional name="display">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2029 <param name="display_selector" value="box" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2030 <param name="use_summit" value="true" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2031 </conditional>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2032 </conditional>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2033 </repeat>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2034 <repeat name="tracks">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2035 <conditional name="track_file_style_conditional">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2036 <param name="track_file_style_selector" value="narrow_peak_track_option" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2037 <param name="title" value="box line_width = 2" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2038 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2039 <param name="color" value="#9bbb59" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2040 <param name="height_narrow_peak" value="4" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2041 <param name="line_width" value="2" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2042 <conditional name="display">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2043 <param name="display_selector" value="box" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2044 <param name="use_summit" value="true" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2045 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2046 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2047 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2048 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2049 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2050 <param name="track_file_style_selector" value="narrow_peak_track_option" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2051 <param name="title" value="peak width 3" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2052 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2053 <param name="color" value="#c0504d" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2054 <param name="height_narrow_peak" value="4" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2055 <conditional name="display">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2056 <param name="display_selector" value="peak" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2057 <param name="use_summit" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2058 <param name="show_data" value="true" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2059 <param name="width_adjust" value="3" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2060 <param name="max_value" value="50" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2061 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2062 <conditional name="labels">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2063 <param name="show_labels" value="false" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2064 </conditional>
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2065 <param name="spacer_height" value="0.5"/>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2066 </conditional>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2067 </repeat>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2068 <repeat name="tracks">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2069 <conditional name="track_file_style_conditional">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2070 <param name="track_file_style_selector" value="narrow_peak_track_option" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2071 <param name="title" value="peak no data range" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2072 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2073 <param name="color" value="#000000" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2074 <param name="height_narrow_peak" value="4" />
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2075 <conditional name="display">
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2076 <param name="display_selector" value="peak" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2077 <param name="use_summit" value="false" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2078 <param name="show_data" value="false" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2079 </conditional>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2080 </conditional>
15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2081 </repeat>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2082 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2083 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2084 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2085 <param name="xaxis_where" value="bottom" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2086 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2087 </repeat>
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2088 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2089 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="image_diff" />
4 15fcad85011e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	2090 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2091 <!--test 7-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2092 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2093 <param name="region" value="chrX:3300000-3500000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2094 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2095 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2096 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2097 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2098 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2099 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2100 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2101 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2102 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2103 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2104 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2105 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2106 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2107 <param name="title" value="gtf default" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2108 <param name="height_bed" value="10" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2109 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2110 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2111 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2112 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2113 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2114 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2115 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2116 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2117 <param name="prefered_name" value="gene_name"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2118 <conditional name="merge_transcripts">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2119 <param name="merge_transcripts_select" value="true"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2120 <param name="merge_overlapping_exons" value="false"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2121 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2122 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2123 <param name="title" value="gtf merge transcripts, use gene_name, red 0.75 UTR" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2124 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2125 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2126 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2127 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2128 <param name="height_utr" value="0.75"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2129 <conditional name="color_utr">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2130 <param name="color_utr_select" value="manually"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2131 <param name="color" value="#ff0000"/>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2132 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2133 </section>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2134 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2135 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2136 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2137 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2138 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2139 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2140 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2141 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2142 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2143 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2144 <param name="prefered_name" value="gene_name"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2145 <conditional name="merge_transcripts">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2146 <param name="merge_transcripts_select" value="true"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2147 <param name="merge_overlapping_exons" value="true"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2148 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2149 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2150 <param name="title" value="same but merge overlapping exons" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2151 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2152 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2153 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2154 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2155 <param name="height_utr" value="0.75"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2156 <conditional name="color_utr">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2157 <param name="color_utr_select" value="manually"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2158 <param name="color" value="#ff0000"/>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2159 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2160 </section>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2161 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2162 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2163 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2164 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2165 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2166 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2167 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2168 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2169 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2170 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2171 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2172 <param name="title" value="genes with scores" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2173 <param name="height_bed" value="10" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2174 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2175 <param name="color_bed_select" value="colormap" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2176 <param name="color" value="cool_r" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2177 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2178 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2179 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2180 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2181 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2182 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2183 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2184 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2185 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2186 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2187 <param name="title" value="genes with utr as bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2188 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2189 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2190 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2191 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2192 <conditional name="color_utr">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2193 <param name="color_utr_select" value="bed_rgb"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2194 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2195 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2196 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2197 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2198 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2199 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2200 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2201 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2202 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2203 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2204 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2205 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2206 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2207 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2208 <param name="height_bed" value="10" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2209 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2210 <param name="color_bed_select" value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2211 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2212 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2213 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2214 <param name="plot_labels" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2215 <param name="labels_in_margin" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2216 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2217 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2218 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2219 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2220 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2221 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2222 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2223 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2224 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2225 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2226 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2227 <param name="title" value="genes bed_rgb like - all_labels_inside" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2228 <param name="height_bed" value="10" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2229 <conditional name="color_bed">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2230 <param name="color_bed_select" value="bed_rgb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2231 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2232 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2233 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2234 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2235 <conditional name="color_utr">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2236 <param name="color_utr_select" value="like"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2237 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2238 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2239 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2240 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2241 <param name="plot_labels" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2242 <param name="all_labels_inside" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2243 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2244 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2245 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2246 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2247 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2248 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2249 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2250 <!--test 8-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2251 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2252 <param name="region" value="chrX:3300000-3500000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2253 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2254 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2255 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2256 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2257 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2258 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2259 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2260 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2261 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2262 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2263 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2264 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2265 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2266 <param name="title" value="global max row max 15 labels" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2267 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2268 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2269 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2270 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2271 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2272 <param name="global_max_row" value="true" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2273 <param name="max_labels" value="15" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2274 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2275 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2276 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2277 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2278 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2279 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2280 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2281 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2282 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2283 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2284 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2285 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2286 <param name="title" value="arrow_interval 10 line_width 2 change color_arrow" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2287 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2288 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2289 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2290 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2291 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2292 <param name="arrow_interval" value="10"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2293 <param name="line_width" value="2"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2294 <conditional name="color_arrow">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2295 <param name="color" value="#00ffff"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2296 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2297 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2298 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2299 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2300 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2301 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2302 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2303 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2304 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2305 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2306 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2307 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2308 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2309 <param name="title" value="same as above but arrowhead_fraction = 0.02" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2310 <param name="height_bed" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2311 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2312 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2313 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2314 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2315 <param name="arrow_interval" value="10"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2316 <param name="line_width" value="2"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2317 <conditional name="color_arrow">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2318 <param name="color" value="#00ffff"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2319 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2320 <param name="arrowhead_fraction" value="0.02"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2321 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2322 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2323 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2324 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2325 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2326 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2327 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2328 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2329 <!--test 9-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2330 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2331 <param name="region" value="X:3133000-3138000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2332 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2333 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2334 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2335 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2336 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2337 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2338 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2339 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2340 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2341 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2342 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2343 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2344 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2345 <param name="title" value="defaut arrowhead fontstyle italic" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2346 <param name="height_bed" value="10" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2347 <param name="spacer_height" value="1"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2348 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2349 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2350 <param name="fontstyle" value="italic"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2351 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2352 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2353 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2354 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2355 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2356 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2357 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2358 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2359 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2360 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2361 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2362 <param name="title" value="arrowhead_fraction 0.1 fontstyle oblique" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2363 <param name="height_bed" value="10" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2364 <param name="spacer_height" value="1"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2365 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2366 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2367 <param name="fontstyle" value="oblique"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2368 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2369 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2370 <param name="arrowhead_fraction" value="0.1"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2371 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2372 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2373 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2374 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2375 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2376 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2377 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2378 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2379 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2380 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2381 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2382 <param name="title" value="genes without orientation" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2383 <param name="height_bed" value="10" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2384 <conditional name="color_bed">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2385 <param name="color_bed_select" value="manually" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2386 <param name="color" value="red" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2387 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2388 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2389 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2390 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2391 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2392 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2393 <param name="spacer_height" value="1"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2394 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2395 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2396 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2397 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2398 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2399 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2400 <param name="input_bed_or_gtf" value="gtf"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2401 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2402 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2403 <param name="title" value="arrowhead included" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2404 <param name="height_bed" value="10" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2405 <conditional name="color_bed">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2406 <param name="color_bed_select" value="manually" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2407 <param name="color" value="red" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2408 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2409 <param name="spacer_height" value="1"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2410 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2411 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2412 <param name="arrowhead_included" value="true"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2413 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2414 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2415 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2416 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2417 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2418 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2419 <param name="track_file_style_selector" value="vlines_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2420 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2421 <param name="line_width" value="2"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2422 <param name="zorder" value="100"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2423 <param name="color" value="red"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2424 </conditional>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2425 </repeat>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2426 <repeat name="tracks">
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2427 <conditional name="track_file_style_conditional">
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2428 <param name="track_file_style_selector" value="vlines_track_option" />
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2429 <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" />
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2430 <param name="line_width" value="5"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2431 <param name="zorder" value="-100"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2432 <param name="color" value="blue"/>
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	2433 <param name="line_style" value="solid"/>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2434 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2435 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2436 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2437 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2438 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2439 <!--test 10-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2440 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2441 <param name="region" value="X:3340000-3380000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2442 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2443 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2444 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2445 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2446 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2447 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2448 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2449 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2450 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2451 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2452 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2453 <param name="track_input_bed" value="domains.bed" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2454 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2455 <param name="height_bed" value="6" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2456 <conditional name="color_bed">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2457 <param name="color_bed_select" value="manually" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2458 <param name="color" value="yellow" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2459 </conditional>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2460 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2461 <param name="display" value="triangles" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2462 <param name="line_width" value="3"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2463 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2464 <param name="spacer_height" value="1"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2465 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2466 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2467 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2468 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2469 <param name="track_file_style_selector" value="bedgraph_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2470 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2471 <param name="title" value="bedgraph" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2472 <param name="height_bedgraph" value="4" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2473 <param name="color" value="blue" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2474 <conditional name="type_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2475 <param name="type_selector" value="line_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2476 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2477 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2478 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2479 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2480 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2481 <param name="track_file_style_selector" value="bedgraph_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2482 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2483 <param name="title" value="bedgraph" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2484 <param name="height_bedgraph" value="4" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2485 <param name="color" value="blue" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2486 <param name="use_middle" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2487 <conditional name="type_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2488 <param name="type_selector" value="line_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2489 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2490 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2491 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2492 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2493 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2494 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2495 <!--test 11-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2496 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2497 <param name="region" value="chrX:3250000-3400000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2498 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2499 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2500 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2501 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2502 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2503 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2504 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2505 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2506 <param name="track_file_style_selector" value="hic_matrix_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2507 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2508 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2509 <!--<param name="colormap" value="RdYlBu_r" />-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2510 <param name="depth" value="100000" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2511 <param name="transform" value="log1p" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2512 <param name="show_masked_bins" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2513 <param name="scale_factor" value="2.0" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2514 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2515 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2516 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2517 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2518 <param name="track_file_style_selector" value="spacer_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2519 <param name="spacer_height" value="0.05" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2520 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2521 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2522 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2523 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2524 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2525 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2526 <param name="title" value="TAD separation score (Ramirez et al.) as block with horizontal lines and data range" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2527 <param name="height_bedgraph" value="10" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2528 <conditional name="type">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2529 <param name="type_selector" value="lines" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2530 <param name="pos_score_in_bin" value="block" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2531 <param name="plot_horizontal_lines" value="true" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2532 <param name="show_data" value="true" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2533 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2534 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2535 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2536 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2537 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2538 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2539 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2540 <param name="title" value="TAD separation score (Ramirez et al.) as center without horizontal lines, summary in red and individual in blue" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2541 <param name="height_bedgraph" value="10" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2542 <conditional name="type">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2543 <param name="type_selector" value="lines" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2544 <param name="pos_score_in_bin" value="center" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2545 <param name="plot_horizontal_lines" value="false" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2546 <param name="individual_color" value="blue"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2547 <param name="summary_color" value="red"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2548 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2549 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2550 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2551 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2552 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2553 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2554 <!--test 12-->
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2555 <test>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2556 <param name="region" value="chrX:3000000-3300000"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2557 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2558 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2559 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2560 <param name="xaxis_where" value="top" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2561 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2562 </repeat>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2563 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2564 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2565 <param name="track_file_style_selector" value="hic_matrix_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2566 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2567 <param name="title" value="Kc DpnII (Li et al. 2015)" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2568 <param name="colormap" value="Purples" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2569 <param name="depth" value="190000" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2570 <param name="transform" value="no" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2571 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2572 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2573 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2574 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2575 <param name="track_file_style_selector" value="link_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2576 <param name="track_input_link" value="test.arcs" ftype="bed" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2577 <param name="title" value="" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2578 <param name="line_width" value="10" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2579 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2580 <param name="links_type" value="loops" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2581 </conditional>
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2582 <conditional name="color_link">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2583 <param name="color_link_select" value="manually" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2584 <param name="color" value="red" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2585 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2586 <param name="overlay_select" value="share-y" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2587 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2588 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2589 <repeat name="tracks">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2590 <conditional name="track_file_style_conditional">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2591 <param name="track_file_style_selector" value="link_track_option" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2592 <param name="track_input_link" value="test.arcs" ftype="bed" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2593 <param name="title" value="" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2594 <param name="height" value="5" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2595 <conditional name="color_link">
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2596 <param name="color_link_select" value="colormap" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2597 <param name="color" value="hot" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2598 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2599 <param name="max_value" value="5"/>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2600 <param name="invert_orientation" value="true" />
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2601 </conditional>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2602 </repeat>
0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2603 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2604 <output name="outFileName" file="test_link.png" ftype="png" compare="image_diff" />
5 0082bb149d37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	2605 </test>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2606 <!--test 13-->
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2607 <test>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2608 <param name="region" value="chrX:3000000-3300000"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2609 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2610 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2611 <param name="track_file_style_selector" value="link_track_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2612 <param name="track_input_link" value="test.arcs" ftype="bed" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2613 <param name="title" value="default" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2614 <conditional name="color_link">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2615 <param name="color_link_select" value="manually" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2616 <param name="color" value="#000000" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2617 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2618 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2619 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2620 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2621 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2622 <param name="track_file_style_selector" value="link_track_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2623 <param name="track_input_link" value="test.arcs" ftype="bed" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2624 <param name="title" value="ylim 20kb" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2625 <conditional name="color_link">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2626 <param name="color_link_select" value="manually" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2627 <param name="color" value="#000000" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2628 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2629 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2630 <param name="ylim" value="20000" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2631 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2632 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2633 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2634 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2635 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2636 <param name="track_file_style_selector" value="link_track_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2637 <param name="track_input_link" value="test.arcs" ftype="bed" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2638 <param name="title" value="compacted" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2639 <conditional name="color_link">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2640 <param name="color_link_select" value="manually" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2641 <param name="color" value="#000000" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2642 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2643 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2644 <param name="compact_arcs_level" value="1" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2645 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2646 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2647 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2648 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2649 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2650 <param name="track_file_style_selector" value="link_track_option" />
14 d640aa8a24ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b iuc parents: 13 diff changeset	2651 <param name="track_input_link" value="test.arcs,test.arcs" ftype="bed" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2652 <param name="title" value="highly compacted" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2653 <conditional name="color_link">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2654 <param name="color_link_select" value="manually" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2655 <param name="color" value="#000000" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2656 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2657 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2658 <param name="compact_arcs_level" value="2" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2659 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2660 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2661 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2662 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2663 <output name="outFileName" file="test_link2.png" ftype="png" compare="image_diff" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2664 </test>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2665 <!--test 14-->
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2666 <test>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2667 <param name="region" value="chrX:3000000-3300000"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2668 <section name="global_args">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2669 <param name="title" value="Scale bar"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2670 <param name="trackLabelFraction" value="0.5"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2671 <param name="trackLabelHAlign" value="center"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2672 </section>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2673 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2674 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2675 <param name="track_file_style_selector" value="spacer_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2676 <param name="spacer_height" value="1.0" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2677 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2678 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2679 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2680 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2681 <param name="track_file_style_selector" value="scale_bar_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2682 <param name="title" value="default" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2683 <param name="spacer_height" value="1"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2684 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2685 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2686 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2687 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2688 <param name="track_file_style_selector" value="scale_bar_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2689 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2690 <param name="color" value="red"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2691 <param name="alpha" value="0.5"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2692 <param name="line_width" value="2"/>
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	2693 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	2694 <param name="x_center" value="3200000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	2695 <param name="size" value="100002"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	2696 </section>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2697 <param name="sb_where" value="right"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2698 <param name="fontsize" value="8"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2699 <param name="spacer_height" value="4"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2700 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2701 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2702 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2703 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="image_diff" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2704 </test>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2705 <!--test 15-->
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2706 <test>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2707 <param name="region" value="chrX:3300000-3500000"/>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2708 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2709 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2710 <param name="track_file_style_selector" value="xaxis_option" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2711 <param name="xaxis_where" value="bottom" />
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2712 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2713 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2714 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2715 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2716 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2717 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2718 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2719 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2720 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2721 <param name="title" value="flybase backbone blue" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2722 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2723 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2724 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2725 <param name="bed_style_select" value="flybase"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2726 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2727 <conditional name="backbone_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2728 <param name="backbone_color_bed_select" value="manually" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2729 <param name="color" value="blue" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2730 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2731 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2732 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2733 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2734 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2735 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2736 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2737 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2738 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2739 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2740 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2741 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2742 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2743 <param name="title" value="UCSC backbone blue" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2744 <param name="height_bed" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2745 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2746 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2747 <param name="bed_style_select" value="UCSC"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2748 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2749 <param name="arrow_interval" value="10"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2750 <conditional name="backbone_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2751 <param name="backbone_color_bed_select" value="manually" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2752 <param name="color" value="blue" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2753 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2754 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2755 </conditional>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	2756 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2757 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2758 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2759 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2760 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2761 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2762 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2763 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2764 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2765 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2766 <param name="title" value="tssarrow" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2767 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2768 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2769 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2770 <param name="bed_style_select" value="tssarrow"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2771 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2772 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2773 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2774 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2775 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2776 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2777 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2778 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2779 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2780 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2781 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2782 <param name="title" value="tssarrow 20kb increase arrowhead" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2783 <param name="height_bed" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2784 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2785 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2786 <param name="bed_style_select" value="tssarrow"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2787 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2788 <param name="arrow_length" value="20000"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2789 <param name="arrowhead_fraction" value="0.01"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2790 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2791 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2792 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2793 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2794 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2795 <repeat name="tracks">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2796 <conditional name="track_file_style_conditional">
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2797 <param name="track_file_style_selector" value="gene_track_option" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2798 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2799 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2800 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2801 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2802 <param name="title" value="exonarrows" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2803 <conditional name="color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2804 <param name="color_bed_select" value="manually" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2805 <param name="color" value="red"/>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2806 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2807 <param name="height_bed" value="10" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2808 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2809 <conditional name="bed_style">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2810 <param name="bed_style_select" value="exonarrows"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2811 <conditional name="border_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2812 <param name="border_color_bed_select" value="manually"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2813 <param name="color" value="red"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2814 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2815 <section name="bed_advanced">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2816 <param name="line_width" value="2" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2817 <conditional name="color_utr">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2818 <param name="color_utr_select" value="manually"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2819 <param name="color" value="blue"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2820 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2821 <conditional name="color_arrow">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2822 <param name="color" value="white"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2823 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2824 </section>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2825 </conditional>
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2826 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2827 </conditional>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2828 </repeat>
d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2829 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2830 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="image_diff" />
7 d691445a7d2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2831 </test>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2832 <!--test 16-->
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2833 <test>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2834 <param name="region" value="chrX:2700000-3100000"/>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2835 <section name="global_args">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2836 <param name="decreasingXAxis" value="true"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2837 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2838 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2839 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2840 <param name="track_file_style_selector" value="bigwig_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2841 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2842 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig color=red alpha = 0.5 max over 300 bins)" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2843 <param name="height_bigwig" value="7" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2844 <param name="color" value="#00b0f0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2845 <section name="reading_bw_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2846 <param name="number_of_bins" value="2000"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2847 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2848 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2849 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2850 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2851 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2852 <param name="track_file_style_selector" value="bigwig_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2853 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2854 <param name="title" value="" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2855 <param name="color" value="#ff0000" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2856 <param name="alpha" value="0.5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2857 <section name="reading_bw_conditional">
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2858 <param name="summary_method" value="max" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2859 <param name="number_of_bins" value="300"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2860 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2861 <param name="overlay_select" value="share-y"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2862 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2863 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2864 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2865 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2866 <param name="track_file_style_selector" value="xaxis_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2867 <param name="xaxis_where" value="bottom" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2868 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2869 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2870 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2871 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="image_diff" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2872 </test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2873 <!--test 17-->
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2874 <test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2875 <param name="region" value="chr2:73,800,000-75,744,000"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2876 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2877 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2878 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2879 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2880 <param name="title" value="bedgraph color = blue transform = no" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2881 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2882 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2883 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2884 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2885 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2886 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2887 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2888 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2889 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2890 <param name="title" value="bedgraph color = blue transform = log" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2891 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2892 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2893 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2894 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2895 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2896 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2897 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2898 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2899 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2900 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2901 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2902 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2903 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2904 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2905 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2906 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2907 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2908 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2909 <param name="min_value" value="1" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2910 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2911 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2912 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2913 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2914 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2915 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2916 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2917 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2918 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2919 <param name="color" value="green" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2920 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2921 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2922 <param name="log_pseudocount" value="2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2923 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2924 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2925 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2926 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2927 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2928 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2929 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2930 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2931 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2932 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2933 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2934 <param name="color" value="green" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2935 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2936 <param name="operation" value="log(2+file)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2937 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2938 <param name="min_value" value="0.7" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2939 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2940 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2941 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2942 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2943 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2944 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2945 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2946 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2947 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2948 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2949 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2950 <param name="transform_selector" value="log2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2951 <param name="log_pseudocount" value="1"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2952 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2953 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2954 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2955 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2956 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2957 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2958 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2959 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2960 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2961 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2962 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2963 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2964 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2965 <param name="operation" value="log2(1+file)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2966 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2967 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2968 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2969 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2970 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2971 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2972 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2973 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2974 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2975 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2976 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2977 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2978 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2979 <param name="transform_selector" value="log2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2980 <param name="log_pseudocount" value="1"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2981 <param name="y_axis_values" value="original"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2982 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2983 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2984 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2985 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2986 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2987 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2988 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2989 <param name="track_file_style_selector" value="xaxis_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2990 <param name="xaxis_where" value="bottom" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2991 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2992 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2993 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	2994 <output name="outFileName" file="test_log.png" ftype="png" compare="image_diff" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2995 </test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2996 <!--test 18-->
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2997 <test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2998 <param name="region" value="chrX:2700000-3100000"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2999 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3000 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3001 <param name="track_file_style_selector" value="xaxis_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3002 <param name="xaxis_where" value="top" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3003 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3004 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3005 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3006 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3007 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3008 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3009 <param name="title" value="file summary_method = mean number_of_bins=20" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3010 <param name="height_bedgraph" value="4" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3011 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3012 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3013 <section name="reading_bdg_as_bw" >
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3014 <param name="summary_method" value="mean" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3015 <param name="number_of_bins" value="20" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3016 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3017 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3018 <param name="max_value" value="30" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3019 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3020 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3021 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3022 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3023 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3024 <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3025 <param name="title" value="second_file summary_method = mean" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3026 <param name="height_bedgraph" value="4" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3027 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3028 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3029 <section name="reading_bdg_as_bw" >
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3030 <param name="summary_method" value="mean" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3031 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3032 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3033 <param name="max_value" value="30" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3034 <param name="spacer_height" value="0.5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3035 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3036 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3037 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3038 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3039 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3040 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3041 <param name="title" value="operation = log1p(file) (no summary_method)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3042 <param name="height_bedgraph" value="4" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3043 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3044 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3045 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3046 <param name="operation" value="log1p(file)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3047 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3048 <param name="spacer_height" value="0.5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3049 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3050 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3051 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3052 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3053 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3054 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3055 <param name="title" value="operation = file - second_file" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3056 <param name="height_bedgraph" value="8" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3057 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3058 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3059 <conditional name="color_negative">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3060 <param name="color_negative_select" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3061 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3062 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3063 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3064 <param name="operation" value="file - second_file" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3065 <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3066 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3067 <param name="min_value" value="-30" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3068 <param name="max_value" value="30" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3069 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3070 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3071 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3072 <output name="outFileName" file="test_operation.png" ftype="png" compare="image_diff" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3073 </test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3074 <!--test 19-->
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3075 <test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3076 <param name="region" value="chr2:73,800,000-75,744,000"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3077 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3078 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3079 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3080 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3081 <param name="title" value="bedgraph color = blue transform = no" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3082 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3083 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3084 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3085 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3086 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3087 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3088 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3089 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3090 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3091 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3092 <param name="title" value="bedgraph color = blue transform = log" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3093 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3094 <param name="color" value="blue" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3095 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3096 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3097 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3098 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3099 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3100 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3101 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3102 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3103 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3104 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3105 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3106 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3107 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3108 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3109 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3110 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3111 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3112 <param name="min_value" value="1" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3113 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3114 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3115 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3116 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3117 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3118 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3119 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3120 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3121 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3122 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3123 <param name="color" value="green" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3124 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3125 <param name="transform_selector" value="log"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3126 <param name="log_pseudocount" value="2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3127 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3128 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3129 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3130 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3131 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3132 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3133 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3134 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3135 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3136 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3137 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3138 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3139 <param name="color" value="green" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3140 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3141 <param name="operation" value="log(2+file)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3142 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3143 <param name="min_value" value="0.7" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3144 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3145 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3146 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3147 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3148 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3149 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3150 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3151 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3152 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3153 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3154 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3155 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3156 <param name="transform_selector" value="log2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3157 <param name="log_pseudocount" value="1"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3158 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3159 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3160 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3161 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3162 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3163 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3164 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3165 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3166 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3167 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3168 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3169 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3170 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3171 <section name="op">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3172 <param name="operation" value="log2(1+file)" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3173 </section>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3174 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3175 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3176 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3177 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3178 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3179 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3180 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3181 <param name="track_file_style_selector" value="bedgraph_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3182 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3183 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3184 <param name="height_bedgraph" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3185 <param name="color" value="black" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3186 <conditional name="logScale_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3187 <param name="transform_selector" value="log2"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3188 <param name="log_pseudocount" value="1"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3189 <param name="y_axis_values" value="original"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3190 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3191 <param name="min_value" value="0" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3192 <param name="show_data" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3193 <param name="grid" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3194 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3195 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3196 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3197 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3198 <param name="track_file_style_selector" value="xaxis_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3199 <param name="xaxis_where" value="bottom" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3200 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3201 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3202 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3203 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="image_diff" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3204 </test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3205 <!--test 20-->
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3206 <test>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3207 <param name="region" value="chrX:3000000-3300000"/>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3208 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3209 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3210 <param name="track_file_style_selector" value="xaxis_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3211 <param name="xaxis_where" value="top" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3212 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3213 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3214 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3215 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3216 <param name="track_file_style_selector" value="spacer_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3217 <param name="spacer_height" value="0.05" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3218 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3219 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3220 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3221 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3222 <param name="track_file_style_selector" value="hic_matrix_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3223 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3224 <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3225 <param name="depth" value="300000" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3226 <param name="transform" value="log1p" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3227 <param name="min_value" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3228 <param name="show_masked_bins" value="false" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3229 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3230 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3231 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3232 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3233 <param name="track_file_style_selector" value="link_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3234 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3235 <conditional name="color_link">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3236 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3237 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3238 <param name="line_width" value="5" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3239 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3240 <param name="links_type" value="loops" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3241 </conditional>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3242 <param name="overlay_select" value="share-y" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3243 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3244 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3245 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3246 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3247 <param name="track_file_style_selector" value="link_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3248 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3249 <conditional name="color_link">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3250 <param name="color" value="RdYlGn" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3251 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3252 <param name="line_width" value="3" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3253 <param name="invert_orientation" value="true" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3254 <param name="title" value="links line_width = 3 color RdYlGn" />
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3255 <param name="height" value="3" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3256 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3257 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3258 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3259 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3260 <param name="track_file_style_selector" value="spacer_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3261 <param name="spacer_height" value="1" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3262 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3263 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3264 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3265 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3266 <param name="track_file_style_selector" value="hic_matrix_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3267 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3268 <param name="title" value="depth = 300000 transform = log1p min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3269 <param name="depth" value="300000" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3270 <param name="transform" value="log1p" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3271 <param name="min_value" value="5" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3272 <param name="show_masked_bins" value="false" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3273 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3274 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3275 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3276 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3277 <param name="track_file_style_selector" value="link_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3278 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3279 <conditional name="color_link">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3280 <param name="color" value="red" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3281 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3282 <param name="line_width" value="5" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3283 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3284 <param name="links_type" value="loops" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3285 </conditional>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3286 <param name="overlay_select" value="share-y" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3287 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3288 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3289 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3290 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3291 <param name="track_file_style_selector" value="link_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3292 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3293 <conditional name="color_link">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3294 <param name="color" value="RdYlGn" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3295 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3296 <param name="line_width" value="3" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3297 <param name="invert_orientation" value="true" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3298 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3299 <param name="use_middle" value="true" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3300 </conditional>
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3301 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3302 <param name="height" value="3" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3303 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3304 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3305 <repeat name="tracks">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3306 <conditional name="track_file_style_conditional">
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3307 <param name="track_file_style_selector" value="vlines_track_option" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3308 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3309 <param name="line_width" value="3" />
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3310 </conditional>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3311 </repeat>
345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3312 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3313 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="image_diff" />
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3314 </test>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3315 <!--test 21-->
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3316 <test>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3317 <param name="region" value="X:3000000-3600000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3318 <section name="global_args">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3319 <param name="trackLabelFraction" value="0.3"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3320 <param name="plotWidth" value="12"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3321 <param name="dpi" value="20"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3322 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3323 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3324 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3325 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3326 <param name="title" value="scalebar where = right" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3327 <param name="sb_where" value="right"/>
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3328 <param name="spacer_height" value="0.5"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3329 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3330 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3331 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3332 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3333 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3334 <param name="title" value="scalebar scalebar_start_position = 3200000" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3335 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3336 <param name="scalebar_start_position" value="3200000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3337 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3338 <param name="spacer_height" value="0.5"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3339 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3340 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3341 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3342 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3343 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3344 <param name="title" value="scalebar scalebar_start_position = 3200000 scalebar_end_position = 3250000" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3345 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3346 <param name="scalebar_start_position" value="3200000"/>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3347 <param name="scalebar_end_position" value="3250000"/>
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3348 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3349 <param name="spacer_height" value="0.5"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3350 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3351 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3352 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3353 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3354 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3355 <param name="title" value="scalebar scalebar_start_position = 3200000 x_center = 3250000" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3356 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3357 <param name="scalebar_start_position" value="3200000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3358 <param name="x_center" value="3250000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3359 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3360 <param name="spacer_height" value="0.5"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3361 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3362 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3363 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3364 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3365 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3366 <param name="title" value="scalebar scalebar_start_position = 3200000 size = 50000" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3367 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3368 <param name="scalebar_start_position" value="3200000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3369 <param name="size" value="50000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3370 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3371 <param name="spacer_height" value="0.5"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3372 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3373 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3374 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3375 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3376 <param name="track_file_style_selector" value="scale_bar_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3377 <param name="title" value="scalebar scalebar_end_position = 3200000 size = 50000" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3378 <section name="scalebar_pos">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3379 <param name="scalebar_end_position" value="3200000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3380 <param name="size" value="50000"/>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3381 </section>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3382 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3383 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3384 <repeat name="tracks">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3385 <conditional name="track_file_style_conditional">
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3386 <param name="track_file_style_selector" value="xaxis_option" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3387 <param name="xaxis_where" value="bottom" />
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3388 </conditional>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3389 </repeat>
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3390 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3391 <output name="outFileName" file="master_scale_bar_startend.png" ftype="png" compare="image_diff" />
8 345d24273a58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	3392 </test>
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3393 <!--test 22-->
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3394 <test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3395 <param name="region" value="chrM:10-30"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3396 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3397 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3398 <param name="track_file_style_selector" value="scale_bar_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3399 <param name="title" value="scalebar height = 5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3400 <param name="sb_where" value="right"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3401 <param name="height" value="5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3402 <param name="spacer_height" value="0.5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3403 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3404 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3405 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3406 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3407 <param name="track_file_style_selector" value="fasta_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3408 <param name="title" value="fasta from cached" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3409 <conditional name="fasta_source">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3410 <param name="fasta_source_selector" value="cached"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3411 <param name="fasta_cached" value="chrM"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3412 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3413 <param name="spacer_height" value="0.5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3414 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3415 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3416 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3417 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3418 <param name="track_file_style_selector" value="fasta_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3419 <param name="title" value="fasta from history height = 5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3420 <conditional name="fasta_source">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3421 <param name="fasta_source_selector" value="history"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3422 <param name="fasta_local" value="chrM.fa" ftype="fasta" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3423 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3424 <param name="height" value="5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3425 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3426 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3427 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3428 <output name="outFileName" file="master_fasta.png" ftype="png" compare="image_diff" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3429 </test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3430 <!--test 23-->
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3431 <test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3432 <param name="region" value="chrX:3000000-3300000"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3433 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3434 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3435 <param name="track_file_style_selector" value="xaxis_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3436 <param name="xaxis_where" value="top" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3437 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3438 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3439 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3440 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3441 <param name="track_file_style_selector" value="spacer_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3442 <param name="spacer_height" value="0.05" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3443 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3444 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3445 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3446 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3447 <param name="track_file_style_selector" value="hic_matrix_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3448 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3449 <param name="title" value="classical depth=300000 with arcs" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3450 <param name="depth" value="300000" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3451 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3452 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3453 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3454 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3455 <param name="track_file_style_selector" value="link_track_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3456 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3457 <conditional name="color_link">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3458 <param name="color" value="red" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3459 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3460 <param name="line_width" value="5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3461 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3462 <param name="links_type" value="loops" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3463 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3464 <param name="overlay_select" value="share-y" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3465 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3466 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3467 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3468 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3469 <param name="track_file_style_selector" value="hic_matrix_square_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3470 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3471 <param name="title" value="square with arcs" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3472 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3473 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3474 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3475 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3476 <param name="track_file_style_selector" value="link_track_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3477 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3478 <conditional name="color_link">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3479 <param name="color" value="red" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3480 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3481 <param name="line_width" value="5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3482 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3483 <param name="links_type" value="squares" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3484 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3485 <param name="overlay_select" value="share-y" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3486 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3487 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3488 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3489 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3490 <param name="track_file_style_selector" value="hic_matrix_square_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3491 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3492 <param name="title" value="square with arcs region2=chrX:3000000-3100000" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3493 <param name="region2" value="chrX:3000000-3100000"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3494 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3495 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3496 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3497 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3498 <param name="track_file_style_selector" value="link_track_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3499 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3500 <conditional name="color_link">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3501 <param name="color" value="red" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3502 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3503 <param name="line_width" value="5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3504 <conditional name="display">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3505 <param name="links_type" value="squares" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3506 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3507 <param name="overlay_select" value="share-y" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3508 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3509 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3510 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3511 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3512 <param name="track_file_style_selector" value="hic_matrix_square_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3513 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3514 <param name="title" value="square with domains, colormap = Blues, tranform = no, region2=chrX:3000000-3100000" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3515 <param name="region2" value="chrX:3000000-3100000"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3516 <param name="colormap" value="Blues"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3517 <param name="transform" value="no" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3518 <param name="boundaries_file" value="tad_classification.bed" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3519 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3520 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3521 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3522 <output name="outFileName" file="test_matrix_square.png" ftype="png" compare="image_diff" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3523 </test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3524 <!--test 24-->
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3525 <test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3526 <param name="region" value="2:34704975-34705208"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3527 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3528 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3529 <param name="track_file_style_selector" value="maf_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3530 <param name="track_input_maf" value="first.maf" ftype="maf"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3531 <param name="reference" value="mm10"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3532 <param name="title" value="default" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3533 <param name="spacer_height" value="1"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3534 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3535 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3536 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3537 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3538 <param name="track_file_style_selector" value="maf_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3539 <param name="track_input_maf" value="first.maf" ftype="maf"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3540 <param name="reference" value="mm10"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3541 <param name="title" value="height = 3 show sequence" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3542 <param name="height" value="3"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3543 <param name="display_ref_seq" value="true"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3544 <param name="spacer_height" value="1"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3545 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3546 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3547 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3548 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3549 <param name="track_file_style_selector" value="maf_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3550 <param name="track_input_maf" value="first.maf" ftype="maf"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3551 <param name="reference" value="mm10"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3552 <param name="title" value="species_order = hg19 rn5, species_labels = Human Rat" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3553 <param name="height" value="3"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3554 <param name="species_order" value="hg19 rn5"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3555 <param name="species_labels" value="Human Rat"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3556 <param name="spacer_height" value="1"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3557 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3558 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3559 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3560 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3561 <param name="track_file_style_selector" value="maf_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3562 <param name="track_input_maf" value="first.maf" ftype="maf"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3563 <param name="reference" value="mm10"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3564 <param name="title" value="species_order = hg19, species_labels = Human, species_order_only = true" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3565 <param name="height" value="3"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3566 <param name="species_order" value="hg19"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3567 <param name="species_labels" value="Human"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3568 <param name="species_order_only" value="true"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3569 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3570 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3571 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3572 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3573 <param name="track_file_style_selector" value="xaxis_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3574 <param name="xaxis_where" value="bottom" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3575 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3576 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3577 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3578 <output name="outFileName" file="test_maf.png" ftype="png" compare="image_diff" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3579 </test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3580 <!--test 25-->
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3581 <test>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3582 <param name="region" value="chr2:73,800,000-75,744,000"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3583 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3584 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3585 <param name="track_file_style_selector" value="bedgraph_track_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3586 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3587 <param name="title" value="bedgraph color = blue" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3588 <param name="height_bedgraph" value="5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3589 <param name="color" value="blue" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3590 <param name="show_data" value="true" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3591 <param name="max_value" value="5" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3592 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3593 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3594 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3595 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3596 <param name="track_file_style_selector" value="vhighlight_track_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3597 <param name="track_input_bed_single" value="islands.bed" ftype="bed"/>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3598 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3599 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3600 <repeat name="tracks">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3601 <conditional name="track_file_style_conditional">
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3602 <param name="track_file_style_selector" value="xaxis_option" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3603 <param name="xaxis_where" value="bottom" />
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3604 </conditional>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3605 </repeat>
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3606 <param name="image_file_format" value="png" />
15 c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3607 <output name="outFileName" file="test_vhighlight.png" ftype="png" compare="image_diff" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3608 </test>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3609 <!--test 26-->
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3610 <test>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3611 <param name="region" value="chrX:3060000-3080000"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3612 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3613 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3614 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3615 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3616 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3617 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3618 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3619 <param name="title" value="default inversions overlayed with empty deletion" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3620 <param name="height_bed" value="2" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3621 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3622 <param name="display" value = "inversions"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3623 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3624 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3625 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3626 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3627 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3628 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3629 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3630 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3631 <param name="track_input_bed" value="empty.bed" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3632 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3633 <param name="title" value="" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3634 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3635 <param name="display" value = "deletions"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3636 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3637 <param name="overlay_select" value="share-y" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3638 <param name="spacer_height" value="1" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3639 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3640 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3641 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3642 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3643 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3644 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3645 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3646 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3647 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3648 <param name="title" value="inversions rgb no labels" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3649 <param name="height_bed" value="2" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3650 <conditional name="color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3651 <param name="color_bed_select" value="bed_rgb" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3652 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3653 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3654 <param name="display" value = "inversions"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3655 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3656 <param name="plot_labels" value = "false"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3657 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3658 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3659 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3660 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3661 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3662 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3663 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3664 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3665 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3666 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3667 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3668 <param name="title" value="deletions colormap no labels" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3669 <param name="height_bed" value="2" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3670 <conditional name="color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3671 <param name="color_bed_select" value="colormap" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3672 <param name="color" value="viridis"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3673 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3674 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3675 <param name="display" value = "deletions"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3676 <conditional name="labels">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3677 <param name="plot_labels" value = "false"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3678 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3679 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3680 <param name="spacer_height" value="1" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3681 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3682 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3683 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3684 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3685 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3686 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3687 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3688 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3689 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3690 <param name="title" value="default deletions" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3691 <param name="height_bed" value="2" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3692 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3693 <param name="display" value = "deletions"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3694 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3695 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3696 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3697 <repeat name="tracks">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3698 <conditional name="track_file_style_conditional">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3699 <param name="track_file_style_selector" value="gene_track_option" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3700 <conditional name="bed_gtf">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3701 <param name="input_bed_or_gtf" value="bed"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3702 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3703 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3704 <param name="title" value="squares border_color orange line_width 3" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3705 <param name="height_bed" value="10" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3706 <conditional name="display_cond">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3707 <param name="display" value="squares"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3708 <param name="line_width" value="3"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3709 <conditional name="border_color_bed">
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3710 <param name="border_color_bed_select" value="manually"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3711 <param name="color" value="orange"/>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3712 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3713 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3714 </conditional>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3715 </repeat>
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3716 <param name="image_file_format" value="png" />
c7af51147b55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 iuc parents: 14 diff changeset	3717 <output name="outFileName" file="test_bed_invdelsquares.png" ftype="png" compare="image_diff" />
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3718 </test>
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3719 </tests>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3720 <help><![CDATA[
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3721
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3722 pyGenomeTracks
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3723 ==============
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3724
2 6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	3725 pyGenomeTracks is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
6aafcf02bd9a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	3726 Currently, it is possible to plot:
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3727
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3728 - bigwig
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3729 - bed/gtf (many options)
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3730 - bedgraph
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3731 - epilogos
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3732 - narrow peaks
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3733 - links
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3734 - Hi-C matrices (cool or HiCExplorer h5)
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3735 - Fasta
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3736 - MAF (multiple alignment format)
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3737
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3738 _________________
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3739
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3740 Usage
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3741 -----
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3742
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3743 This tool takes various types of tracks as input:
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3744
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3745 - Hi-C tracks:
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3746 - TAD vizualisation: corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3747 - TAD score: display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3748 - Chromatin states: display blocks of different colors following a bed file.
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3749 - Gene track / Bed Track: display genes or annotations in bed/gtf files. Labels like gene names can be toggled on or off.
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3750 - Link track: display links (pair of coordinates) as arcs, triangles or loops.
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3751 - NarrowPeak track: display narrowPeak (encode format) as boxes or as curve (reconstructed peak).
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3752 - Bigwig track: generic bigwig track plotting.
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3753 - Bedgraph track: generic bedgraph track plotting.
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3754 - Bedgraph matrix track is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3755 - Vlines: vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3756 - Vhighlight: vertical rectangles drawn on top of all tracks following a bed file. It is used as a visual support to highlight some regions.
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3757 - Hlines: horizontal lines drawn either by themselves or on top of other tracks.
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3758 - Spacer: Add some space between two tracks.
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3759 - X-axis: Plot x-axis scale wherever you want.
42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3760 - Scale bar track: Plot scale bar.
11 2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3761 - Fasta track: Display sequences from fasta.
2f09a07c94ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def iuc parents: 10 diff changeset	3762 - Maf track: Display alignments from maf.
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3763
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3764 For each track, parameters for the color, the width or the font size can be defined.
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3765
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3766 _________________
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3767
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3768 Output
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3769 ------
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3770
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3771 Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used):
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3772
12 ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3773 .. image:: static/images/demo.png
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3774 :width: 45 %
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3775 .. image:: static/images/demo2.png
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3776 :width: 45 %
ca69a2c9afc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 iuc parents: 11 diff changeset	3777
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3778
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3779 _________________
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3780
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3781 \| For more information about pyGenomeTracks please consider our documentation on readthedocs_ or github_
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3782
9 42ac675e0c60 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d1b394c8e588a78d1b94e3e57922f7ce684ac835" iuc parents: 8 diff changeset	3783 .. _readthedocs: https://pygenometracks.readthedocs.io
0 5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3784 .. _github: https://github.com/deeptools/pyGenomeTracks
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3785 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3786 ]]></help>
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3787 <expand macro="citations" />
5141268dba30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3788 </tool>

Mercurial > repos > iuc > pygenometracks

annotate pyGenomeTracks.xml @ 15:c7af51147b55 draft default tip