Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 122:ae07c55ab96b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a9124072bc71dd670ee58ff8e4846e14d6d603ec
author fubar
date Fri, 04 Oct 2024 04:07:03 +0000
parents 794aecef8327
children 137e08517410
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121:478ee3e780de 122:ae07c55ab96b
19 </required_files> 19 </required_files>
20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> 20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
21 <command detect_errors="aggressive"><![CDATA[ 21 <command detect_errors="aggressive"><![CDATA[
22 mkdir -p '$output.files_path' && 22 mkdir -p '$output.files_path' &&
23 cp '$trackxml' '$output.files_path/galaxy.xml' && 23 cp '$trackxml' '$output.files_path/galaxy.xml' &&
24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && 24 export JBROWSE2_PATH=\$(realpath \$(dirname \$(which jbrowse))/../opt/jbrowse2) &&
25 #if $jbgen.ucol.formcoll=="collect": 25 #if $jbgen.ucol.formcoll=="collect":
26 python '$__tool_directory__/autogenJB2.py' 26 python '$__tool_directory__/autogenJB2.py'
27 #for $key in $autoCollection.keys(): 27 #for $key in $autoCollection.keys():
28 #if $autoCollection[$key].is_collection: 28 #if $autoCollection[$key].is_collection:
29 #set subCol=$autoCollection[$key] 29 #set subCol=$autoCollection[$key]