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comparison autogenJB2.xml @ 35:15da358c3108 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Wed, 28 Feb 2024 10:08:57 +0000
parents 8f02a84ee278
children 5f39f745682f
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34:2893ef33fba9 35:15da358c3108
1 <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05"> 1 <tool id="autogenjb2" name="autogenjb2" version="2.10.2_0" profile="22.05">
2 <description>Files to JBrowse2</description> 2 <description>Track collection to JBrowse2</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
7 <xrefs> 7 <xrefs>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command> 11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 python '$__tool_directory__/autogenJB2.py' 13 python '$__tool_directory__/autogenJB2.py'
14 #for $key in $jbrowseme.keys(): 14 #for $key in $autoCollection.keys():
15 --collection '$key,$jbrowseme[$key],$jbrowseme[$key].ext' 15 #if $autoCollection[$key].ext == 'fasta':
16 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
17 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
18 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
19 #else if $autoCollection[$key].ext in ['bam',]
20 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
21 #else if $autoCollection[$key].ext in ['cram',]
22 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
23 #end if
16 #end for 24 #end for
17 --sessName "Autogen JBrowse" 25 --outdir '$output.files_path'
26 --sessName "Autogen JBrowse" &&
27
28 cp '$output.files_path/index.html' '$output'
29
30 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
31
32
18 ]]></command> 33 ]]></command>
19 <inputs> 34 <inputs>
20 <param 35 <param
21 label="Collection of files specially named to become tracks" 36 label="Collection of files to become tracks - they must have short, informative names"
22 name="jbrowseme" 37 name="autoCollection"
23 type="data_collection"> 38 type="data_collection">
24 </param> 39 </param>
25 </inputs> 40 </inputs>
26 <outputs> 41 <outputs>
27 <data format="html" name="output" label="JBrowse2"/> 42 <data format="html" name="output" label="AutoJBrowse2"/>
28 </outputs> 43 </outputs>
29 44
30 <help><![CDATA[ 45 <help><![CDATA[
31 46
32 JBrowse2-in-Galaxy 47 JBrowse2-in-Galaxy