hubarchivecreator: hubArchiveCreator.xml annotate

author	yating-l
date	Mon, 31 Oct 2016 16:36:25 -0400
parents
children	4ced8f116509

rev	line source
0 3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	2 <description>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	3 This Galaxy tool permits to prepare your files to be ready for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	4 Assembly Hub visualization.
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	5 </description>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	6
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	7 <requirements>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	8 <!-- Conda dependencies -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	18 <requirement type="package" version="1.3">samtools</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	19 <!-- ToolShed dependencies -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	20 <requirement type="package" version="312">ucsc_tools</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	26 <requirement type="package" version="1.2">samtools</requirement>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	27 </requirements>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	28
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	29 <stdio>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	30 <regex match="^pass1"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	31 source="stderr"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	32 level="log"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	33 description="bedToBigBed"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	34 <!-- TODO: Add the case pass1 and 0 chroms -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	35 <!-- TODO: Add the case pass2 and 0 records or 0 fields -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	36 </stdio>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	37
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	38 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	39 <command detect_errors="exit_code"><![CDATA[
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	40 mkdir -p $output.extra_files_path;
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	41
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	42 python $__tool_directory__/hubArchiveCreator.py
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	43
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	44 ## Ask the user to enter the genome name
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	45 --genome_name '$genome_name'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	46
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	47 #import json
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	48
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	49 #set global data_parameter_dict = {}
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	50
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	51 ## Function to retrieve the data of the inputs
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	52 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	53 #set false_path = str($input_to_prepare)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	54 #set name = $input_to_prepare.name
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	55
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	56 #set data_dict = {"name": $name}
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	57 #silent data_dict.update($extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	58
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	59 ## Add the ordering by taking the tool form indexes
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	60 #silent $data_dict.update({"order_index": $order_index})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	61
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	62 #silent $data_parameter_dict.update({$false_path: $data_dict})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	63
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	64 #end def
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	65
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	66
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	67 ## Get the number of digits from tracks, to have a unique integer from group index and track index
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	68
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	69 #set temp_max_digit = 0
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	70
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	71 #for $g in $group
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	72 #if len($g.format) > $temp_max_digit
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	73 #silent temp_max_digit = len($g.format)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	74 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	75 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	76
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	77 #set nb_digits_max_track = len(str($temp_max_digit))
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	78
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	79 ## END Get the number of digits
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	80
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	81 #for $i_g, $g in enumerate( $group )
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	82 #for $i, $f in enumerate( $g.format )
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	83 ## Create the order index using index_group+1 concatenated with index_track
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	84 #set index_group_final = str($i_g + 1)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	85 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	86
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	87 ## For each format, we have a few mandatory fields we store in a dict
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	88 #set track_color = str($f.formatChoice.track_color)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	89 #set group_name = str($g.group_name)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	90
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	91 #set extra_data_dict = {"track_color": $track_color,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	92 "group_name": $group_name}
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	93
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	94 #if $f.formatChoice.format_select == "bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	95 --bam $f.formatChoice.BAM
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	96 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	97
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	98 ## Add Bam format specific fields
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	99 #silent extra_data_dict.update({"index": $bam_index})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	100
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	101 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	102 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	103 #if $f.formatChoice.format_select == "bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	104 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	105 --bed $f.formatChoice.bedChoice.BED
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	106 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	107 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	108 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	112 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	113 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	114 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	115 #if $f.formatChoice.format_select == "psl"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	116 --psl $f.formatChoice.PSL
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	117 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	118 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	119 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	120 #if $f.formatChoice.format_select == "bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	121 --bigwig $f.formatChoice.BIGWIG
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	122 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	123 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	124 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	125 #if $f.formatChoice.format_select == "gff3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	126 --gff3 $f.formatChoice.GFF3
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	127 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	128 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	129 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	130 #if $f.formatChoice.format_select == "gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	131 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	132 --gtf $f.formatChoice.GTF
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	133 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	134 extra_data_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	135 #end if
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	136 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	137 #end for
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	138
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	139 ## We combine the fasta file dataset name with his false path in a JSON object
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	140 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	141 -f '$fasta_json'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	142
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	143 ## Dump the final json
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	144 #set all_data_json = json.dumps($data_parameter_dict)
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	145
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	146 --data_json '$all_data_json'
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	147
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	148 ## Retrieve the user email
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	149 --user_email $__user_email__
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	150
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	151 -d $__tool_directory__
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	152
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	153 -e $output.extra_files_path
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	154
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	155 $advanced_options.debug_mode
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	156
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	157 -o $output;
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	158
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	159 ]]></command>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	160
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	161 <inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	162 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	163 name="genome_name"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	164 type="text"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	165 size="30"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	166 value="unknown"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	167 label="UCSC Genome Browser assembly ID"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	168 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	169 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	170 format="fasta"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	171 name="fasta_file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	172 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	173 label="Reference genome"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	174 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	175 <repeat name="group" title="New group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	176 <param type="text" name="group_name" label="Group name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	177 <repeat name="format" title="New track">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	178 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	179 <param name="format_select" type="select" label="Format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	180 <option value="bam" selected="true">BAM</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	181 <option value="bed">BED</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	182 <option value="psl">PSL</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	183 <option value="bigwig">BIGWIG</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	184 <option value="gff3">GFF3</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	185 <option value="gtf">GTF</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	186 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	187
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	188 <when value="bam">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	189 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	190 format="bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	191 name="BAM"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	192 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	193 label="BAM File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	194 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	195 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	196 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	197 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	198 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	199 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	200 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	201 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	202 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	203 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	204 <when value="bed">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	205 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	206 <param name="bed_select" type="select" label="Bed Choice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	209 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	210 <when value="bed_generic">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	211 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	212 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	213 name="BED"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	214 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	215 label="Generic Bed File Choice"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	216 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	217
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	218 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	219 <when value="bed_simple_repeats_option">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	220 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	221 format="bed"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	222 name="BED_simple_repeats"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	223 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	224 label="Bed Simple Repeats (Bed4+12) File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	225 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	226 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	227 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	228 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	229 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	230 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	231 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	232 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	233 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	234 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	235 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	236 <when value="psl">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	237 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	238 format="psl"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	239 name="PSL"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	240 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	241 label="PSL File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	242 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	243 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	244 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	245 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	246 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	247 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	248 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	249 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	250 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	251 <when value="bigwig">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	252 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	253 format="bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	254 name="BIGWIG"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	255 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	256 label="BIGWIG File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	257 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	258 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	259 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	260 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	261 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	262 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	263 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	264 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	265 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	266 <when value="gff3">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	267 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	268 format="gff3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	269 name="GFF3"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	270 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	271 label="GFF3 File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	272 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	273 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	274 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	275 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	276 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	277 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	278 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	279 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	280 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	281 <when value="gtf">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	282 <param
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	283 format="gtf"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	284 name="GTF"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	285 type="data"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	286 label="GTF File"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	287 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	288 <param name="track_color" type="color" label="Track color" value="#000000">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	289 <sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	290 <valid initial="string.letters,string.digits">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	291 <add value="#"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	292 </valid>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	293 </sanitizer>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	294 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	295 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	296 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	297 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	298 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	299 <conditional name="advanced_options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	300 <param name="advanced_options_selector" type="select" label="Advanced options">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	301 <option value="off" selected="true">Hide advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	302 <option value="on">Display advanced options</option>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	303 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	304 <!-- TODO: Avoid redundancy here -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	305 <when value="on">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	306 <param name="debug_mode" type="boolean"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	307 label="Activate debug mode" checked="false"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	308 truevalue="--debug_mode" falsevalue="">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	309 <help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	310 Use this option if you are a G-OnRamp developer
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	311 </help>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	312 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	313 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	314 <when value="off">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	315 <param name="debug_mode" type="hidden"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	316 value="">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	317 </param>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	318 </when>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	319 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	320 </inputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	321
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	322 <outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	323 <data format="trackhub" name="output"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	324 </outputs>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	325
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	326 <tests>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	327 <!-- Test with only the fasta file -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	328 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	329 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	330 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	331 <output name="output" file="only_genome/only_genome.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	332 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	333 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	334 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	335 <!-- Email could be different, but we need to ensure we still have the email line -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	336 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	337 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	338 <has_text text="email"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	339 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	340 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	341 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	342 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	343 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	344 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	345 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	346
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	347 <!-- Test with Bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	348 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	349 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	350 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	351 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	352 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	353 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	354 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	355 <param name="format_select" value="bam"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	356 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	357 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	358 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	359 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	360 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	361 <output name="output" file="bam/bam.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	362 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	363 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	364 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	365 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	366 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	367 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	368 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	369 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	370 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	371 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	372 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	373 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	374 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	375 <assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	376 <has_text text="track"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	377 <has_text text="longLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	378 <has_text text="shortLabel"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	379 <has_text text="bigDataUrl"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	380 <has_text text="type"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	381 <has_text text="visibility"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	382 <has_text text="thickDrawItem"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	383 <has_text text="priority"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	384 <has_text text="color"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	385 <has_text text="group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	386 </assert_contents>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	387 </extra_files>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	388 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	389 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	390 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	391
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	392 <!-- Test with Bed Generic -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	393 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	394 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	395 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	396 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	397 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	398 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	399 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	400 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	401 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	402 <param name="bed_select" value="bed_generic"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	403 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	404 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	405 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	406 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	407 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	408 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	409 <output name="output" file="bed_generic/bed_generic.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	410 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	411 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	412 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	413 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	414 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	415 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	416 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	417 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	418
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	419 <!-- Test with Bed Simple repeat -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	420 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	421 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	422 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	423 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	424 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	425 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	426 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	427 <param name="format_select" value="bed" />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	428 <conditional name="bedChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	429 <param name="bed_select" value="bed_simple_repeats_option"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	430 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	431 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	432 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	433 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	434 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	435 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	436 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	437 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	438 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	439 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	440 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	441 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	442 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	443 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	444 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	445 <!-- Test with Psl -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	446 <!-- Test with BigWig -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	447 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	448 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	449 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	450 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	451 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	452 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	453 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	454 <param name="format_select" value="bigwig"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	455 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	456 <param name="track_color" value="#000000"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	457 </conditional>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	458 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	459 </repeat>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	460 <output name="output" file="bigwig/bigwig.html">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	461 <!-- Verify tracks folder contains bam and bai -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	462 <extra_files type="file"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	463 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	464 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	465 compare="sim_size"
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	466 />
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	467 <!-- Verify trackDb.txt contains the basic fields for a bam -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	468 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	469 </output>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	470 </test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	471
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	472 <!-- Test with GFF3 -->
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	473 <test>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	474 <param name="genome_name" value="Dbia3"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	475 <param name="fasta_file" value="common/dbia3.fa"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	476 <repeat name="group">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	477 <param name="group_name" value="Default group"/>
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	478 <repeat name="format">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	479 <conditional name="formatChoice">
3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty yating-l parents: diff changeset	480 <param name="format_select" value="gff3"/>
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0

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1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">

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2 <description>

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3 This Galaxy tool permits to prepare your files to be ready for

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4 Assembly Hub visualization.

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5 </description>

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6

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7 <requirements>

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8

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9 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>

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10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>

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11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>

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12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>

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13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>

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14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>

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15

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16

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17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>

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18 <requirement type="package" version="1.3">samtools</requirement>

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19

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20 <requirement type="package" version="312">ucsc_tools</requirement>

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21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>

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22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>

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23 <requirement type="package" version="0.0.1">genePredToBed</requirement>

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24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>

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25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>

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26 <requirement type="package" version="1.2">samtools</requirement>

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27 </requirements>

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28

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29 <stdio>

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30 <regex match="^pass1"

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31 source="stderr"

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32 level="log"

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33 description="bedToBigBed"/>

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34

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35

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36 </stdio>

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37

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38

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39 <command detect_errors="exit_code"><![CDATA[

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40 mkdir -p $output.extra_files_path;

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41

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42 python $__tool_directory__/hubArchiveCreator.py

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43

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44 ## Ask the user to enter the genome name

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45 --genome_name '$genome_name'

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46

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47 #import json

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48

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49 #set global data_parameter_dict = {}

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50

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51 ## Function to retrieve the data of the inputs

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52 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})

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53 #set false_path = str($input_to_prepare)

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54 #set name = $input_to_prepare.name

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55

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56 #set data_dict = {"name": $name}

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57 #silent data_dict.update($extra_data_dict)

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58

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59 ## Add the ordering by taking the tool form indexes

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60 #silent $data_dict.update({"order_index": $order_index})

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61

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62 #silent $data_parameter_dict.update({$false_path: $data_dict})

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63

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64 #end def

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65

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66

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67 ## Get the number of digits from tracks, to have a unique integer from group index and track index

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68

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69 #set temp_max_digit = 0

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70

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71 #for $g in $group

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72 #if len($g.format) > $temp_max_digit

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73 #silent temp_max_digit = len($g.format)

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74 #end if

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75 #end for

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76

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77 #set nb_digits_max_track = len(str($temp_max_digit))

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78

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79 ## END Get the number of digits

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80

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81 #for $i_g, $g in enumerate( $group )

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82 #for $i, $f in enumerate( $g.format )

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83 ## Create the order index using index_group+1 concatenated with index_track

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84 #set index_group_final = str($i_g + 1)

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85 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)

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86

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87 ## For each format, we have a few mandatory fields we store in a dict

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88 #set track_color = str($f.formatChoice.track_color)

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89 #set group_name = str($g.group_name)

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90

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91 #set extra_data_dict = {"track_color": $track_color,

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92 "group_name": $group_name}

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93

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94 #if $f.formatChoice.format_select == "bam"

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95 --bam $f.formatChoice.BAM

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96 #set bam_index = $f.formatChoice.BAM.metadata.bam_index

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97

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98 ## Add Bam format specific fields

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99 #silent extra_data_dict.update({"index": $bam_index})

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100

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101 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)

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102 #end if

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103 #if $f.formatChoice.format_select == "bed"

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104 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"

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105 --bed $f.formatChoice.bedChoice.BED

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106 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,

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107 extra_data_dict)

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108 #end if

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109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"

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110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats

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111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,

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112 extra_data_dict)

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113 #end if

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114 #end if

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115 #if $f.formatChoice.format_select == "psl"

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116 --psl $f.formatChoice.PSL

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117 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,

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118 extra_data_dict)

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119 #end if

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120 #if $f.formatChoice.format_select == "bigwig"

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121 --bigwig $f.formatChoice.BIGWIG

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122 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,

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123 extra_data_dict)

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124 #end if

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125 #if $f.formatChoice.format_select == "gff3"

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126 --gff3 $f.formatChoice.GFF3

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127 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,

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128 extra_data_dict)

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129 #end if

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130 #if $f.formatChoice.format_select == "gtf"

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131 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8

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132 --gtf $f.formatChoice.GTF

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133 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,

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134 extra_data_dict)

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135 #end if

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136 #end for

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137 #end for

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138

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139 ## We combine the fasta file dataset name with his false path in a JSON object

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140 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})

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141 -f '$fasta_json'

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142

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143 ## Dump the final json

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144 #set all_data_json = json.dumps($data_parameter_dict)

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145

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146 --data_json '$all_data_json'

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147

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148 ## Retrieve the user email

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149 --user_email $__user_email__

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150

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151 -d $__tool_directory__

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152

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153 -e $output.extra_files_path

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154

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155 $advanced_options.debug_mode

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156

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157 -o $output;

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158

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159 ]]></command>

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160

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161 <inputs>

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162 <param

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163 name="genome_name"

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164 type="text"

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165 size="30"

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166 value="unknown"

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167 label="UCSC Genome Browser assembly ID"

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168 />

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169 <param

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170 format="fasta"

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171 name="fasta_file"

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172 type="data"

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173 label="Reference genome"

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174 />

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175 <repeat name="group" title="New group">

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176 <param type="text" name="group_name" label="Group name" value="Default group"/>

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177 <repeat name="format" title="New track">

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178 <conditional name="formatChoice">

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179 <param name="format_select" type="select" label="Format">

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180 <option value="bam" selected="true">BAM</option>

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181 <option value="bed">BED</option>

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182 <option value="psl">PSL</option>

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183 <option value="bigwig">BIGWIG</option>

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184 <option value="gff3">GFF3</option>

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185 <option value="gtf">GTF</option>

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186 </param>

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187

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188 <when value="bam">

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189 <param

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190 format="bam"

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191 name="BAM"

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192 type="data"

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193 label="BAM File"

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194 />

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195

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196 <param name="track_color" type="color" label="Track color" value="#000000">

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197 <sanitizer>

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198 <valid initial="string.letters,string.digits">

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199 <add value="#"/>

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200 </valid>

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201 </sanitizer>

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202 </param>

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203 </when>

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204 <when value="bed">

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205 <conditional name="bedChoice">

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206 <param name="bed_select" type="select" label="Bed Choice">

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207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>

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208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>

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209 </param>

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210 <when value="bed_generic">

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211 <param

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212 format="bed"

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213 name="BED"

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214 type="data"

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215 label="Generic Bed File Choice"

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216 />

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217

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218 </when>

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219 <when value="bed_simple_repeats_option">

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220 <param

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221 format="bed"

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222 name="BED_simple_repeats"

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223 type="data"

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224 label="Bed Simple Repeats (Bed4+12) File"

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225 />

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226 </when>

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227 </conditional>

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228 <param name="track_color" type="color" label="Track color" value="#000000">

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229 <sanitizer>

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230 <valid initial="string.letters,string.digits">

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231 <add value="#"/>

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232 </valid>

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233 </sanitizer>

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234 </param>

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235 </when>

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236 <when value="psl">

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237 <param

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238 format="psl"

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239 name="PSL"

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240 type="data"

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241 label="PSL File"

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242 />

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243 <param name="track_color" type="color" label="Track color" value="#000000">

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244 <sanitizer>

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245 <valid initial="string.letters,string.digits">

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246 <add value="#"/>

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247 </valid>

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248 </sanitizer>

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249 </param>

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250 </when>

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251 <when value="bigwig">

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252 <param

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253 format="bigwig"

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254 name="BIGWIG"

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255 type="data"

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256 label="BIGWIG File"

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257 />

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258 <param name="track_color" type="color" label="Track color" value="#000000">

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259 <sanitizer>

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260 <valid initial="string.letters,string.digits">

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261 <add value="#"/>

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262 </valid>

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263 </sanitizer>

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264 </param>

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265 </when>

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266 <when value="gff3">

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267 <param

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268 format="gff3"

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269 name="GFF3"

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270 type="data"

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271 label="GFF3 File"

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272 />

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273 <param name="track_color" type="color" label="Track color" value="#000000">

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274 <sanitizer>

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275 <valid initial="string.letters,string.digits">

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276 <add value="#"/>

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277 </valid>

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278 </sanitizer>

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279 </param>

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280 </when>

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281 <when value="gtf">

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282 <param

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283 format="gtf"

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284 name="GTF"

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285 type="data"

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286 label="GTF File"

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287 />

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288 <param name="track_color" type="color" label="Track color" value="#000000">

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289 <sanitizer>

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290 <valid initial="string.letters,string.digits">

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291 <add value="#"/>

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292 </valid>

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293 </sanitizer>

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294 </param>

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295 </when>

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296 </conditional>

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297 </repeat>

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298 </repeat>

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299 <conditional name="advanced_options">

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300 <param name="advanced_options_selector" type="select" label="Advanced options">

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301 <option value="off" selected="true">Hide advanced options</option>

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302 <option value="on">Display advanced options</option>

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303 </param>

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304

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305 <when value="on">

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306 <param name="debug_mode" type="boolean"

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307 label="Activate debug mode" checked="false"

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308 truevalue="--debug_mode" falsevalue="">

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309 <help>

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310 Use this option if you are a G-OnRamp developer

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311 </help>

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312 </param>

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313 </when>

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314 <when value="off">

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315 <param name="debug_mode" type="hidden"

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316 value="">

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317 </param>

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318 </when>

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319 </conditional>

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320 </inputs>

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321

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322 <outputs>

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323 <data format="trackhub" name="output"/>

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324 </outputs>

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325

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326 <tests>

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327

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328 <test>

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329 <param name="genome_name" value="Dbia3"/>

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330 <param name="fasta_file" value="common/dbia3.fa"/>

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331 <output name="output" file="only_genome/only_genome.html">

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332 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" />

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333 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" />

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334 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>

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335

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336 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">

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337 <assert_contents>

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338 <has_text text="email"/>

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339 </assert_contents>

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340 </extra_files>

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341 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">

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342 </extra_files>

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343 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>

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344 </output>

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345 </test>

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346

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347

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348 <test>

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349 <param name="genome_name" value="Dbia3"/>

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350 <param name="fasta_file" value="common/dbia3.fa"/>

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351 <repeat name="group">

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352 <param name="group_name" value="Default group"/>

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353 <repeat name="format">

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354 <conditional name="formatChoice">

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355 <param name="format_select" value="bam"/>

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356 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />

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357 <param name="track_color" value="#000000"/>

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358 </conditional>

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359 </repeat>

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360 </repeat>

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361 <output name="output" file="bam/bam.html">

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362

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363 <extra_files type="file"

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364 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"

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365 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"

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366 compare="sim_size"

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367 />

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368 <extra_files type="file"

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369 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"

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370 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"

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371 compare="sim_size"

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372 />

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373

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374 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt">

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375 <assert_contents>

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376 <has_text text="track"/>

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377 <has_text text="longLabel"/>

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378 <has_text text="shortLabel"/>

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379 <has_text text="bigDataUrl"/>

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380 <has_text text="type"/>

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381 <has_text text="visibility"/>

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382 <has_text text="thickDrawItem"/>

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383 <has_text text="priority"/>

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384 <has_text text="color"/>

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385 <has_text text="group"/>

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386 </assert_contents>

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387 </extra_files>

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388

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389 </output>

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390 </test>

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391

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392

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393 <test>

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394 <param name="genome_name" value="Dbia3"/>

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395 <param name="fasta_file" value="common/dbia3.fa"/>

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396 <repeat name="group">

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397 <param name="group_name" value="Default group"/>

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398 <repeat name="format">

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399 <conditional name="formatChoice">

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400 <param name="format_select" value="bed" />

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401 <conditional name="bedChoice">

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402 <param name="bed_select" value="bed_generic"/>

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403 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>

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404 <param name="track_color" value="#000000"/>

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405 </conditional>

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406 </conditional>

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407 </repeat>

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408 </repeat>

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409 <output name="output" file="bed_generic/bed_generic.html">

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410

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411 <extra_files type="file"

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412 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"

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413 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"

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414 compare="sim_size"

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415 />

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416 </output>

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417 </test>

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418

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419

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420 <test>

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421 <param name="genome_name" value="Dbia3"/>

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422 <param name="fasta_file" value="common/dbia3.fa"/>

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423 <repeat name="group">

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424 <param name="group_name" value="Default group"/>

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425 <repeat name="format">

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426 <conditional name="formatChoice">

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427 <param name="format_select" value="bed" />

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428 <conditional name="bedChoice">

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429 <param name="bed_select" value="bed_simple_repeats_option"/>

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430 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>

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431 <param name="track_color" value="#000000"/>

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432 </conditional>

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433 </conditional>

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434 </repeat>

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435 </repeat>

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436 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">

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437

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438 <extra_files type="file"

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439 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"

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440 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"

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441 compare="sim_size"

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442 />

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443 </output>

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444 </test>

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445

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446

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447 <test>

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448 <param name="genome_name" value="Dbia3"/>

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449 <param name="fasta_file" value="common/dbia3.fa"/>

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450 <repeat name="group">

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451 <param name="group_name" value="Default group"/>

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452 <repeat name="format">

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453 <conditional name="formatChoice">

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454 <param name="format_select" value="bigwig"/>

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455 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>

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456 <param name="track_color" value="#000000"/>

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457 </conditional>

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458 </repeat>

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459 </repeat>

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460 <output name="output" file="bigwig/bigwig.html">

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461

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462 <extra_files type="file"

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463 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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464 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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465 compare="sim_size"

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466 />

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467

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468

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469 </output>

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470 </test>

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471

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472

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473 <test>

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474 <param name="genome_name" value="Dbia3"/>

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475 <param name="fasta_file" value="common/dbia3.fa"/>

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476 <repeat name="group">

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477 <param name="group_name" value="Default group"/>

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478 <repeat name="format">

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479 <conditional name="formatChoice">

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480 <param name="format_select" value="gff3"/>

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481 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>

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482 <param name="track_color" value="#000000"/>

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483 </conditional>

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484 </repeat>

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485 </repeat>

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486 <output name="output" file="gff3/gff3_trackhub.html">

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487

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488 <extra_files type="file"

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489 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"

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490 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"

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491 compare="sim_size"

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492 />

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493

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494

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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495 </output>

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496 </test>

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497

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498

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499 <test>

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500 <param name="genome_name" value="Dbia3"/>

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501 <param name="fasta_file" value="common/dbia3.fa"/>

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502 <repeat name="group">

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503 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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504 <repeat name="format">

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505 <conditional name="formatChoice">

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506 <param name="format_select" value="gtf"/>

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507 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>

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508 <param name="track_color" value="#000000"/>

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509 </conditional>

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510 </repeat>

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511 </repeat>

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512 <output name="output" file="gtf/gtf_trackhub.html">

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513

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514 <extra_files type="file"

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515 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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516 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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517 compare="sim_size"

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518 />

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519

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520

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521 </output>

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522 </test>

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523

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524

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525 <test>

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526 <param name="genome_name" value="Dbia3"/>

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527 <param name="fasta_file" value="common/dbia3.fa"/>

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528 <repeat name="group">

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529 <param name="group_name" value="Default group"/>

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530 <repeat name="format">

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531 <conditional name="formatChoice">

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diff changeset

532 <param name="format_select" value="gtf"/>

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533 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>

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534 <param name="track_color" value="#000000"/>

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535 </conditional>

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536 </repeat>

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537 <repeat name="format">

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538 <conditional name="formatChoice">

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539 <param name="format_select" value="gff3"/>

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540 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>

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541 <param name="track_color" value="#000000"/>

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542 </conditional>

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543 </repeat>

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544 </repeat>

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545 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">

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546

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547 <extra_files type="file"

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548 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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549 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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diff changeset

550 compare="sim_size"

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551 />

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552 <extra_files type="file"

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553 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"

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554 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"

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diff changeset

555 compare="sim_size"

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556 />

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557

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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558

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559 </output>

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diff changeset

560 </test>

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561

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diff changeset

562

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563

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diff changeset

564

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

565 <test>

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566 <param name="genome_name" value="Dbia3"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

567 <param name="fasta_file" value="common/dbia3.fa"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

568 <repeat name="group">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

parents:

diff changeset

569 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

570 </repeat>

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diff changeset

571 <repeat name="group">

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yating-l

parents:

diff changeset

572 <param name="group_name" value="Other group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

573 </repeat>

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diff changeset

574 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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diff changeset

575 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

576 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

577

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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diff changeset

578 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

579 <assert_contents>

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yating-l

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580 <has_text text="email"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

581 </assert_contents>

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diff changeset

582 </extra_files>

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diff changeset

583 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

584 </extra_files>

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yating-l

parents:

diff changeset

585 <extra_files type="file" name="myHub/Dbia3/description.html"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

586 value="two_groups_no_track/myHub/Dbia3/description.html"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

587 </output>

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diff changeset

588 </test>

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diff changeset

589

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yating-l

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diff changeset

590

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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diff changeset

591 <test>

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diff changeset

592 <param name="genome_name" value="Dbia3"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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593 <param name="fasta_file" value="common/dbia3.fa"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

594 <repeat name="group">

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diff changeset

595 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

596 <repeat name="format">

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diff changeset

597 <conditional name="formatChoice">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

598 <param name="format_select" value="bigwig"/>

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diff changeset

599 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

600 <param name="track_color" value="#000000"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

601 </conditional>

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diff changeset

602 </repeat>

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diff changeset

603 </repeat>

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604 <repeat name="group">

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diff changeset

605 <param name="group_name" value="Other group"/>

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606 </repeat>

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607 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">

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608

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609 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>

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610 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>

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611

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612 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">

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613 <assert_contents>

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614 <has_text text="email"/>

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615 </assert_contents>

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616 </extra_files>

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617 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">

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618 </extra_files>

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619 <extra_files type="file" name="myHub/Dbia3/description.html"

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620 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>

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621

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622

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623 <extra_files type="file"

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624 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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625 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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626 compare="sim_size"

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627 />

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628

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629

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630 </output>

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631 </test>

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632

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633

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634 <test>

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635 <param name="genome_name" value="Dbia3"/>

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636 <param name="fasta_file" value="common/dbia3.fa"/>

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637 <repeat name="group">

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638 <param name="group_name" value="Default group"/>

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639 <repeat name="format">

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640 <conditional name="formatChoice">

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641 <param name="format_select" value="bigwig"/>

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642 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>

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643 <param name="track_color" value="#000000"/>

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644 </conditional>

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645 </repeat>

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646 </repeat>

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647 <repeat name="group">

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648 <param name="group_name" value="Other group"/>

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649 <repeat name="format">

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650 <conditional name="formatChoice">

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651 <param name="format_select" value="gtf"/>

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652 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>

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653 <param name="track_color" value="#000000"/>

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654 </conditional>

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655 </repeat>

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656 </repeat>

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657 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">

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658

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659 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>

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660 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>

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661

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662 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"

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663 lines_diff="2">

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664 <assert_contents>

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665 <has_text text="email"/>

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666 </assert_contents>

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667 </extra_files>

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668 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">

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669 </extra_files>

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670 <extra_files type="file" name="myHub/Dbia3/description.html"

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671 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>

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672

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673

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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674

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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675 <extra_files type="file"

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676 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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677 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

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678 compare="sim_size"

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679 />

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680

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681

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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682 <extra_files type="file"

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683 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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684 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

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685 compare="sim_size"

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686 />

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687

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688 </output>

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689 </test>

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690

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691

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692 <test>

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693 <param name="genome_name" value="Dbia3"/>

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694 <param name="fasta_file" value="common/dbia3.fa"/>

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695 <repeat name="group">

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696 <param name="group_name" value="Default group"/>

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697 <repeat name="format">

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698 <conditional name="formatChoice">

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699 <param name="format_select" value="bigwig"/>

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700 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/>

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701 <param name="track_color" value="#000000"/>

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702 </conditional>

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703 </repeat>

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704 <repeat name="format">

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705 <conditional name="formatChoice">

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diff changeset

706 <param name="format_select" value="bam"/>

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diff changeset

707 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>

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diff changeset

708 <param name="track_color" value="#000000"/>

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diff changeset

709 </conditional>

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710 </repeat>

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711 </repeat>

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712 <repeat name="group">

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diff changeset

713 <param name="group_name" value="Other group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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714 <repeat name="format">

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diff changeset

715 <conditional name="formatChoice">

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diff changeset

716 <param name="format_select" value="gtf"/>

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diff changeset

717 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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718 <param name="track_color" value="#000000"/>

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719 </conditional>

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720 </repeat>

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721 <repeat name="format">

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722 <conditional name="formatChoice">

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diff changeset

723 <param name="format_select" value="gff3"/>

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diff changeset

724 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/>

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725 <param name="track_color" value="#000000"/>

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726 </conditional>

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727 </repeat>

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728 </repeat>

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729 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">

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730

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yating-l

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731 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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732 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>

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733

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734 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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735 lines_diff="2">

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diff changeset

736 <assert_contents>

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737 <has_text text="email"/>

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diff changeset

738 </assert_contents>

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diff changeset

739 </extra_files>

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diff changeset

740 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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741 </extra_files>

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diff changeset

742 <extra_files type="file" name="myHub/Dbia3/description.html"

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743 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>

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744

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diff changeset

745

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746

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747 <extra_files type="file"

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diff changeset

748 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

749 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

750 compare="sim_size"

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diff changeset

751 />

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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752 <extra_files type="file"

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diff changeset

753 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

754 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

755 compare="sim_size"

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diff changeset

756 />

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

757 <extra_files type="file"

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diff changeset

758 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"

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diff changeset

759 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

760 compare="sim_size"

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diff changeset

761 />

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762

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763

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764 <extra_files type="file"

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765 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

766 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

767 compare="sim_size"

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diff changeset

768 />

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769 <extra_files type="file"

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770 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

771 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

772 compare="sim_size"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

773 />

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diff changeset

774

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diff changeset

775 </output>

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diff changeset

776 </test>

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diff changeset

777

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diff changeset

778

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parents:

diff changeset

779 <test>

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diff changeset

780 <param name="genome_name" value="Dbia3"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

781 <param name="fasta_file" value="common/dbia3.fa"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

782 <repeat name="group">

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diff changeset

783 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

784 <repeat name="format">

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diff changeset

785 <conditional name="formatChoice">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

786 <param name="format_select" value="bam"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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parents:

diff changeset

787 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

788 <param name="track_color" value="#000000"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

789 </conditional>

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diff changeset

790 </repeat>

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791 </repeat>

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792 <output name="output" file="default_color/default_color_trackhub.html">

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793

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794 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">

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795 <assert_contents>

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796 <has_text text="color 0,0,0"/>

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diff changeset

797 </assert_contents>

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798 </extra_files>

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diff changeset

799

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diff changeset

800

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diff changeset

801 </output>

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diff changeset

802 </test>

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803

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diff changeset

804

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diff changeset

805 <test>

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diff changeset

806 <param name="genome_name" value="Dbia3"/>

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807 <param name="fasta_file" value="common/dbia3.fa"/>

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diff changeset

808 <repeat name="group">

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diff changeset

809 <param name="group_name" value="Default group"/>

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diff changeset

810 <repeat name="format">

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diff changeset

811 <conditional name="formatChoice">

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diff changeset

812 <param name="format_select" value="bam"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

813 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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814 <param name="track_color" value="#8064a2"/>

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diff changeset

815 </conditional>

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diff changeset

816 </repeat>

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817 </repeat>

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818 <output name="output" file="changed_color/changed_color_trackhub.html">

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819

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diff changeset

820 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">

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diff changeset

821 <assert_contents>

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822 <has_text text="color 128,100,162"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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823 </assert_contents>

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diff changeset

824 </extra_files>

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diff changeset

825

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diff changeset

826

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diff changeset

827 </output>

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diff changeset

828 </test>

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diff changeset

829

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diff changeset

830

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diff changeset

831 <test>

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diff changeset

832 <param name="genome_name" value="Dbia3"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

833 <param name="fasta_file" value="common/dbia3.fa"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

834 <repeat name="group">

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parents:

diff changeset

835 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

836 <repeat name="format">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

837 <conditional name="formatChoice">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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parents:

diff changeset

838 <param name="format_select" value="gtf"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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parents:

diff changeset

839 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

840 <param name="track_color" value="#000000"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

841 </conditional>

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diff changeset

842 </repeat>

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diff changeset

843 </repeat>

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diff changeset

844 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

845 <extra_files type="file"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

846 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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parents:

diff changeset

847 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

848 compare="sim_size"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

849 />

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diff changeset

850

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

851

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

852 </output>

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diff changeset

853 </test>

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diff changeset

854

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diff changeset

855

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diff changeset

856 <test>

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diff changeset

857 <param name="genome_name" value="Dbia3"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

858 <param name="fasta_file" value="common/dbia3.fa"/>

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diff changeset

859 <repeat name="group">

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parents:

diff changeset

860 <param name="group_name" value="Default group"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

861 <repeat name="format">

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diff changeset

862 <conditional name="formatChoice">

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diff changeset

863 <param name="format_select" value="bed" />

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864 <conditional name="bedChoice">

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diff changeset

865 <param name="bed_select" value="bed_generic"/>

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866 <param name="BED" ftype="bed" value="bed_generic/inputs/testing"/>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

867 <param name="track_color" value="#000000"/>

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diff changeset

868 </conditional>

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869 </conditional>

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diff changeset

870 </repeat>

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diff changeset

871 </repeat>

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diff changeset

872 <output name="output" file="bed_generic/bed_generic2.html">

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diff changeset

873

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diff changeset

874 <extra_files type="file"

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diff changeset

875 name="myHub/Dbia3/tracks/testing.bb"

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diff changeset

876 value="bed_generic/myHub/Dbia3/tracks/testing.bb"

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

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diff changeset

877 compare="sim_size"

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diff changeset

878 />

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parents:

diff changeset

879 </output>

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diff changeset

880 </test>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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881

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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882

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

parents:

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883

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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884

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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885 </tests>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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886

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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887 <help>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

parents:

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888 This Galaxy tool permits to prepare your files to be ready for

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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889 Assembly Hub visualization.

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

parents:

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890 </help>

3e0c61b52a06 planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

yating-l

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891 </tool>

Mercurial > repos > yating-l > hubarchivecreator

annotate hubArchiveCreator.xml @ 0:3e0c61b52a06 draft