circos: circgraph.xml annotate

annotate circgraph.xml @ 1:95664f8de269 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 24c6ef0ca00b91b3f184a5cce3ad0f9435b27b46

author	iuc
date	Thu, 04 Oct 2018 06:05:11 -0400
parents	8464186c8503
children

rev	line source
0 8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	1 <?xml version="1.0"?>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	2 <tool id="circgraph" name="Circos Builder" version="@WRAPPER_VERSION@">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	3 <description>creates circos plots from standard bioinformatics datatypes.</description>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	4 <macros>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	5 <import>macros.xml</import>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	6 <import>macros_conffiles.xml</import>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	7 </macros>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	8 <expand macro="requirements"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	9 <version_command>circos --version</version_command>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	10 <command detect_errors="aggressive"><![CDATA[
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	11 ## Directory structure
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	12 mkdir -p circos/conf/ circos/data/ &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	13
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	14 #if $reference_genome.reference_genome_source == 'history':
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	15 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	16 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	17
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	18 #if $reference_genome.reference_genome_source != 'karyotype':
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	19 ## Process the karyotype.txt file
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	20 python '$__tool_directory__/fasta-to-karyotype.py'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	21
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	22 #if str($reference_genome.reference_genome_source) == 'cached':
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	23 '${reference_genome.fasta_indexes.fields.path}'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	24 #else if str($reference_genome.reference_genome_source) == 'history':
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	25 genomeref.fa
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	26 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	27
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	28 #if $reference_genome.bands:
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	29 '${reference_genome.bands}'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	30 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	31 > circos/conf/karyotype.txt &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	32 #else
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	33 cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	34 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	35
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	36 mv '$circos_conf' circos/conf/circos.conf &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	37 mv '$ticks_conf' circos/conf/ticks.conf &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	38 mv '$ideogram_conf' circos/conf/ideogram.conf &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	39 mv '$data_conf' circos/conf/2d.conf &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	40 mv '$links_conf' circos/conf/links.conf &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	41 mv '$test_case_conf' circos/conf/galaxy_test_case.xml &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	42
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	43 ## 2D Data Plots
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	44 #for $hi, $data in enumerate($sec_tdd.data):
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	45 #if str($data.plot_format.plot_format_select) == 'tile':
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	46 python '$__tool_directory__/unified-tiles.py'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	47 '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	48 > circos/data/data-${hi}.txt &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	49 #else:
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	50 python $__tool_directory__/unified-histogram.py
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	51 $data.plot_format.plot_format_select
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	52 #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	53 #for $fi, $file in enumerate($data.plot_format.data_source):
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	54 '${file}' '${file.ext}'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	55 #end for
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	56 #else:
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	57 '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	58 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	59 > circos/data/data-${hi}.txt &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	60 #end if
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	61 #end for
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	62
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	63 ## Link Tracks
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	64 #for $hi, $data in enumerate($sec_links.data):
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	65 cp '${data.data_source}' circos/data/links-${hi}.txt &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	66 #end for
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	67
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	68 tar cvfz circos.tar.gz circos &&
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	69
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	70 circos -conf circos/conf/circos.conf
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	71 ]]></command>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	72 <configfiles>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	73 <expand macro="configfile_circos_conf" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	74 <expand macro="configfile_ticks_conf" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	75 <expand macro="configfile_ideogram_conf" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	76 <expand macro="configfile_data_conf" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	77 <expand macro="configfile_links_conf" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	78 <expand macro="test_case" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	79 </configfiles>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	80 <inputs>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	81 <conditional name="reference_genome">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	82 <param name="reference_genome_source" type="select" label="Reference Genome">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	83 <option value="history" selected="True">From History</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	84 <option value="cached">Locally Cached</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	85 <option value="karyotype">Karyotype</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	86 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	87 <when value="cached">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	88 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	89 <options from_data_table="all_fasta"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	90 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	91 <!-- TODO: multiple band files? -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	92 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	93 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	94 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	95 <when value="history">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	96 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	97 <!-- TODO: multiple band files? -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	98 <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	99 help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	100 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	101 <when value="karyotype">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	102 <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	103 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	104 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	105
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	106 <section name="ideogram" title="Ideogram Configuration (Genome/Chromosomes)">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	107 <param name="spacing" type="float" value="0.005" label="Spacing Between Ideograms"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	108 <param name="radius" type="float" value="0.90" label="Radius"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	109 <param name="thickness" type="float" value="10" label="Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	110
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	111 <section name="ideogram_labels" title="Labels">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	112 <param name="show_label" type="boolean" truevalue="yes" falsevalue="no" label="Show Label"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	113 <!--<param type="float" value="0.95" label="Radius" name="radius"/>-->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	114 <!--<param type="float" value="10" label="Thickness" name="thickness"/>-->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	115 <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	116 help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	117 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	118 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	119
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	120 <section name="ticks" title="Ticks">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	121 <param name="show_ticks" type="boolean" truevalue="yes" falsevalue="no" label="Show Ticks"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	122 <!--<param type="boolean" label="Show Tick Labels" name="show_tick_labels" truevalue="true" falsevalue="false" />-->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	123 <param name="radius" type="float" value="1.0" label="Radius"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	124 <expand macro="circos_color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	125 <param name="multiplier" type="float" value="1e-3" label="Multiplier"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	126 help="1e-3 means your tick spacing will be in kb (tick spacing of 5000 = every 5kb, labels will read '5kb'). 1e-6 means mb."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	127
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	128 <repeat name="tick_group" title="Tick Group">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	129 <param name="spacing" type="float" value="5000" label="Tick Spacing" help="Number of bases"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	130 <param name="size" type="float" value="10" label="Tick Size"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	131 <param name="show_tick_labels" type="boolean" truevalue="yes" falsevalue="no" label="Show Tick Labels"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	132 <param name="label_size" type="float" value="20" label="Label Size"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	133 <param name="label_offset" type="float" value="10" label="Label Offset"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	134 <param name="format" type="select" label="Label Format">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	135 <option value="%d" selected="True">Integer</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	136 <option value="%f">Float</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	137 <option value="%.1f">Float (one decimal)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	138 <option value="%.2f">Float (two decimals)</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	139 <sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	140 <valid>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	141 <add value="%" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	142 </valid>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	143 </sanitizer>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	144 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	145 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	146
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	147 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	148
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	149 <section name="sec_tdd" title="2D Data">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	150 <repeat name="data" title="2D Data Plot">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	151 <!-- Positioning -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	152 <param name="r1" type="float" value="0.89" label="Outside Radius"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	153 <param name="r0" type="float" value="0.8" label="Inside Radius"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	154 <param name="orientation" type="boolean" label="Orient Inwards" truevalue="in" falsevalue="out"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	155 help="When yes/true, the plot will face inwards. I.e. lowest values will be to the outside"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	156
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	157 <conditional name="plot_format">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	158 <param name="plot_format_select" type="select" label="Plot Format">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	159 <option value="histogram" selected="True">Histogram</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	160 <option value="heatmap">Heatmap</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	161 <option value="line">Line</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	162 <option value="scatter">Scatter</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	163 <option value="tile">Tiles</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	164 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	165 <when value="histogram">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	166 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Histogram Data Source"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	167 multiple="True" help="If multiple files are selected, they will be treated as a stacked histogram"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	168 <section name="format_specific" title="Plot Format Specific Options">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	169 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	170 <param name="extend_bins" type="boolean" label="Join non-abutting Bins" truevalue="yes" falsevalue="no"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	171 help="Join histogram bins that do not touch (abut)" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	172 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	173 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	174 <when value="heatmap">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	175 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Heatmap Data Source"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	176 multiple="True" help="If multiple files are selected, they will be plotted alongside each other radially"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	177 <section name="format_specific" title="Plot Format Specific Options">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	178 <expand macro="brewer_scale" label="Fill Color" name="fill_color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	179 <param name="scale_log_base" type="float" value="1.0" label="Scale Log Base"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	180 help="If scale_log_base<1, the dynamic range of color mapping of small values will be increased. If scale_log_base>1, then dynamic range of large values will be increased."/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	181 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	182 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	183 <when value="line">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	184 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Line Data Source"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	185 <section name="format_specific" title="Plot Format Specific Options">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	186 <expand macro="circos_color" label="Stroke Color" name="color" value="#000000"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	187 <param name="thickness" type="integer" value="0" label="Stroke Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	188 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	189 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	190 <when value="scatter">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	191 <param name="data_source" type="data" format="bed6,bed12,wig,gff3" label="Scatter Plot Data Source"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	192 <section name="format_specific" title="Plot Format Specific Options">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	193 <!-- glyph, glyph_size, min, max -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	194 <param name="glyph" type="select" label="Glyph">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	195 <option value="circle">Circle</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	196 <option value="triangle">Triangle</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	197 <option value="rectangle">Rectangle</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	198 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	199 <param name="glyph_size" type="integer" value="8" label="Glyph Size"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	200 <param name="data_min" type="float" value="0.0" label="Data Minimum" help="Minimum value of the range of the plot axis, data outside this range are clipped." />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	201 <param name="data_max" type="float" value="1.0" label="Data Maximum" help="Maximum value of the range of the plot axis, data outside this range are clipped." />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	202 <expand macro="circos_color" name="color" value="#555555" label="Color" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	203 <expand macro="circos_color" name="stroke_color" value="#000000" label="Stroke Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	204 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	205 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	206 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	207 <when value="tile">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	208 <param name="data_source" type="data" format="bed6,bed12,gff3" label="Tile Data Source"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	209 help="If your tile source features have scores in them, they will be used in colouration"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	210 <section name="format_specific" title="Plot Format Specific Options">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	211 <expand macro="brewer_scale" name="fill_color" label="Fill Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	212 <expand macro="circos_color" name="color" value="#000000" label="Stroke Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	213 <param name="stroke_thickness" type="integer" value="0" label="Stroke Thickness"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	214 <param name="layers" type="integer" value="15" label="Layers"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	215 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	216 <param name="padding" type="float" value="8" label="Padding" help="In pixels"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	217
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	218 <conditional name="overflow">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	219 <param name="overflow_behavior" type="select" label="Overflow Behavior">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	220 <option value="hide">Hide: overflow tiles are not drawn</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	221 <option value="grow">Grow: new layers are added as required</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	222 <option value="collapse">Collapse: overflow tiles are drawn on the first layer</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	223 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	224 <when value="hide">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	225 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	226 <when value="grow">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	227 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	228 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	229 <when value="collapse">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	230 <expand macro="circos_color" name="layer_overflow_color" label="Layer Overflow Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	231 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	232 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	233 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	234 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	235 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	236
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	237 <expand macro="rules" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	238 <expand macro="axes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	239 <expand macro="backgrounds" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	240 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	241 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	242 <section name="sec_links" title="Link Tracks">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	243 <repeat name="data" title="Link Data">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	244 <!-- Positioning -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	245 <param name="radius" type="float" value="0.8" label="Inside Radius"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	246 help="This is the radial position of the termination of the link; for relative values, if radius smaller than 1 then it is defined in terms of the inner ideogram radius, otherwise it is defined in terms of the outer ideogram radius" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	247 <param name="data_source" type="data" format="txt" label="Link Data Source" help="Select file with link data. Format: chr1 start1 end1 chr2 start2 end2" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	248 <conditional name="linktype">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	249 <param name="ribbon" type="select" label="Link Type" help="">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	250 <option value="no" selected="true">basic</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	251 <option value="yes">ribbon</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	252 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	253 <when value="yes">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	254 <param name="twist" type="select" label="Twist Ribbon">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	255 <option value="" selected="true">auto</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	256 <option value="twist=yes">always</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	257 <option value="flat=yes">never</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	258 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	259 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	260 <when value="no"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	261 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	262 <expand macro="circos_color" name="color" value="#000000" label="Link Color"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	263 <param name="thickness" type="float" value="15" label="Thickness" help="In pixels"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	264 <param name="bezier_radius" type="float" value="0.1" min="0" max="1" label="Bezier Radius"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	265 help="The radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is 0 then straight lines will be used"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	266
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	267 <section name="advanced" title="Advanced Settings">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	268 <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	269 help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple link tracks"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	270 <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	271 help="Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position. In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	272 <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	273 help="The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1)"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	274 <conditional name="perturbation">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	275 <param name="perturb" type="select" label="Perturb links?"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	276 help="A set of parameters can be used to randomly adjust bezier_radius, bezier_radius_purity, and crest parameters to give the links a more disorganized, organic feel. By perturbing each link you can also show additional texture in the data among links which would have ordinarily overlapped. Each parameter's perturbation amount is defined as a pair of values - pmin,pmax. These are the minimum and maximum multipliers by which the value can be perturbed">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	277 <option value="no" selected="true">no</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	278 <option value="yes">yes</option>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	279 </param>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	280 <when value="yes">
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	281 <param name="perturb_crest_min" type="float" value="0.5" label="Crest min"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	282 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	283 <param name="perturb_crest_max" type="float" value="1.5" label="Crest max"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	284 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	285 <param name="perturb_bezier_radius_min" type="float" value="0.5" label="Bezier Radius min"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	286 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	287 <param name="perturb_bezier_radius_max" type="float" value="1.5" label="Bezier Radius max"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	288 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	289 <param name="perturb_bezier_radius_purity_min" type="float" value="0.5" label="Bezier Radius Purity min"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	290 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	291 <param name="perturb_bezier_radius_purity_max" type="float" value="1.5" label="Bezier Radius Purity max"
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	292 help="For example setting (min,max) = (0.5,1.2) will cause parameter to be randomly scaled between 50-120%"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	293 </when>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	294 <when value="no"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	295 </conditional>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	296 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	297 <expand macro="linkrules"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	298 </repeat>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	299 </section>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	300 </inputs>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	301 <outputs>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	302 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (png)"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	303 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (svg)"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	304 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	305 </outputs>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	306 <tests>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	307 <test>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	308 <param name="reference_genome\|reference_genome_source" value="history"/>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	309 <param name="reference_genome\|genome_fasta" value="1/input.fa" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	310 <!-- ideograms -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	311 <param name="ideogram\|spacing" value="0.005" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	312 <param name="ideogram\|radius" value="0.9" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	313 <param name="ideogram\|thickness" value="10.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	314 <param name="ideogram\|ideogram_labels\|show_label" value="yes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	315 <param name="ideogram\|ideogram_labels\|parallel" value="no" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	316 <!-- Ticks -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	317 <param name="ticks\|show_ticks" value="yes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	318 <param name="ticks\|radius" value="1.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	319 <param name="ticks\|color" value="#17365d" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	320 <param name="ticks\|multiplier" value="0.001" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	321 <param name="ticks\|tick_group_0\|tickspacing" value="5000.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	322 <param name="ticks\|tick_group_0\|size" value="20.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	323 <param name="ticks\|tick_group_0\|show_tick_labels" value="yes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	324 <param name="ticks\|tick_group_0\|label_size" value="20.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	325 <param name="ticks\|tick_group_0\|label_offset" value="10.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	326 <param name="ticks\|tick_group_0\|label_format" value="%d" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	327 <param name="ticks\|tick_group_1\|tickspacing" value="500.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	328 <param name="ticks\|tick_group_1\|size" value="10.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	329 <param name="ticks\|tick_group_1\|show_tick_labels" value="no" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	330 <param name="ticks\|tick_group_1\|label_size" value="20.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	331 <param name="ticks\|tick_group_1\|label_offset" value="10.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	332 <param name="ticks\|tick_group_1\|label_format" value="%d" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	333 <!-- Data -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	334 <param name="sec_tdd\|data_0\|r0" value="0.8" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	335 <param name="sec_tdd\|data_0\|r1" value="0.89" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	336 <param name="sec_tdd\|data_0\|orientation" value="out" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	337 <param name="sec_tdd\|data_0\|plot_format\|plot_format_select" value="histogram" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	338 <param name="sec_tdd\|data_0\|plot_format\|data_source" value="1/0-0.wig" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	339 <param name="sec_tdd\|data_0\|plot_format\|format_specific\|fill_color" value="purples-13-seq" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	340 <param name="sec_tdd\|data_0\|plot_format\|format_specific\|extend_bins" value="no" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	341
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	342 <param name="sec_tdd\|data_1\|r0" value="0.7" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	343 <param name="sec_tdd\|data_1\|r1" value="0.79" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	344 <param name="sec_tdd\|data_1\|orientation" value="out" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	345 <param name="sec_tdd\|data_1\|plot_format\|plot_format_select" value="tile" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	346 <param name="sec_tdd\|data_1\|plot_format\|data_source" value="1/1.gff3" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	347 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|fill_color" value="rdylgn-15-div" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	348 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|color" value="#000000" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	349 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|stroke_thickness" value="1" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	350 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|layers" value="15" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	351 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|thickness" value="15.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	352 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|padding" value="8.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	353 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|overflow\|overflow_behavior" value="grow" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	354 <param name="sec_tdd\|data_1\|plot_format\|format_specific\|overflow\|layer_overflow_color" value="#ffc000" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	355
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	356 <param name="sec_tdd\|data_2\|r0" value="0.6" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	357 <param name="sec_tdd\|data_2\|r1" value="0.69" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	358 <param name="sec_tdd\|data_2\|orientation" value="out" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	359 <param name="sec_tdd\|data_2\|plot_format\|plot_format_select" value="scatter" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	360 <param name="sec_tdd\|data_2\|plot_format\|data_source" value="1/2.wig" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	361 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|glyph" value="triangle" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	362 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|glyph_size" value="8" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	363 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|data_min" value="0.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	364 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|data_max" value="1.0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	365 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|color" value="#555555" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	366 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|stroke_color" value="#000000" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	367 <param name="sec_tdd\|data_2\|plot_format\|format_specific\|stroke_thickness" value="0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	368 <!-- Links -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	369 <param name="sec_links\|data_0\|radius" value="0.59" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	370 <param name="sec_links\|data_0\|data_source" value="1/links.txt" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	371 <param name="sec_links\|data_0\|linktype\|ribbon" value="yes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	372 <param name="sec_links\|data_0\|color" value="#9966ff" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	373 <param name="sec_links\|data_0\|bezier_radius" value="0.3" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	374 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|application_select" value="pos1" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	375 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|comparison\|compare" value="lt" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	376 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|conditions_0\|application\|comparison\|compval" value="25000" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	377 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|actions_0\|action\|action_select" value="color" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	378 <param name="sec_links\|data_0\|sec_link_rule\|rules_0\|actions_0\|action\|action_value" value="#ffcc00" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	379
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	380 <param name="sec_links\|data_1\|radius" value="0.45" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	381 <param name="sec_links\|data_1\|data_source" value="1/links2.txt" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	382 <param name="sec_links\|data_1\|linktype\|ribbon" value="yes" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	383 <param name="sec_links\|data_1\|color" value="#42aa42" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	384 <param name="sec_links\|data_1\|bezier_radius" value="0" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	385
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	386 <!-- Outputs -->
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	387 <output name="output_png" file="1/output.png" compare="sim_size" delta="15000" ftype="png" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	388 <output name="output_svg" file="1/output.svg" compare="sim_size" ftype="svg" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	389 </test>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	390 </tests>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	391 <help><![CDATA[
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	392 Circos
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	393 ======
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	394
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	395 Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	396
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	397 Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	398
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	399 .. image:: $PATH_TO_IMAGES/circos-sample-panel.png
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	400 :alt: several example circos plots
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	401
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	402 For more information see the Circos documentation_.
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	403
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	404 .. _documentation: http://circos.ca/documentation/
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	405
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	406
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	407 ]]></help>
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	408 <expand macro="citations" />
8464186c8503 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit a41493893bdcbe330434db9c5851719012b62fa8 iuc parents: diff changeset	409 </tool>

Mercurial > repos > iuc > circos

annotate circgraph.xml @ 1:95664f8de269 draft