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comparison autogenJB2.xml @ 39:bc57164eb270 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
author fubar
date Fri, 01 Mar 2024 01:03:09 +0000
parents 5f39f745682f
children e1a3d3221ed3
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38:07849bf248e3 39:bc57164eb270
8 <xref type="bio.tools">jbrowse2</xref> 8 <xref type="bio.tools">jbrowse2</xref>
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 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
13 python '$__tool_directory__/autogenJB2.py' 14 python '$__tool_directory__/autogenJB2.py'
14 #for $key in $autoCollection.keys(): 15 #for $key in $autoCollection.keys():
15 #if $autoCollection[$key].ext == 'fasta': 16 #if $autoCollection[$key].ext == 'fasta':
16 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key' 17 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
17 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf'] 18 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
21 #else if $autoCollection[$key].ext in ['cram',] 22 #else if $autoCollection[$key].ext in ['cram',]
22 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index' 23 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
23 #end if 24 #end if
24 #end for 25 #end for
25 --outdir '$output.files_path' 26 --outdir '$output.files_path'
27 --jbrowse2path \${JBROWSE2_PATH}
26 --sessName "Autogen JBrowse" && 28 --sessName "Autogen JBrowse" &&
27 29
28 cp '$output.files_path/index.html' '$output' 30 cp '$output.files_path/index.html' '$output'
29 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. 31 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
30 #if str($uglyTestingHack) == "enabled": 32 #if str($uglyTestingHack) == "enabled":