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comparison cuffmerge_wrapper.xml @ 7:4df774d8a900 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
author iuc
date Wed, 23 Oct 2024 22:12:11 +0000
parents f4bc1b2fc4d4
children
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6:f4bc1b2fc4d4 7:4df774d8a900
1 <tool id="cuffmerge" name="Cuffmerge" version="@TOOL_VERSION@.4" profile="@PROFILE@"> 1 <tool id="cuffmerge" name="Cuffmerge" version="@TOOL_VERSION@.5" profile="@PROFILE@">
2 <description>merge together several Cufflinks assemblies</description> 2 <description>merge together several Cufflinks assemblies</description>
3 <macros> 3 <macros>
4 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <version_command>cuffmerge -v</version_command> 7 <version_command>cuffmerge -v</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @CUFFLINKS_LINK_GTF_INPUTS@ 9 @CUFFLINKS_LINK_GTF_INPUTS@
10 echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt && 10 echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/g' > assembly_GTF_list.txt &&
11 cuffmerge 11 cuffmerge
12 -o output 12 -o output
13 --num-threads="\${GALAXY_SLOTS:-4}" 13 --num-threads="\${GALAXY_SLOTS:-4}"
14 ## Use annotation reference? 14 ## Use annotation reference?
15 #if $annotation.use_ref_annotation == "Yes": 15 #if $annotation.use_ref_annotation == "Yes":