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comparison cuffquant_wrapper.xml @ 4:d2daca60e139 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:09:03 -0500
parents 25cf1ab351df
children dd79e9e3aa10
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3:25cf1ab351df 4:d2daca60e139
1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> 1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.1">
2 <!-- Wrapper supports Cuffdiff versions 2.2.1 --> 2 <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
3 <description>Precompute gene expression levels</description> 3 <description>Precompute gene expression levels</description>
4 <macros> 4 <macros>
5 <import>cuff_macros.xml</import> 5 <import>cuff_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <version_command>cuffquant 2>&amp;1 | head -n 1</version_command> 8 <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
10 <command> 9 <command detect_errors="aggressive"><![CDATA[
11 cuffquant 10 cuffquant
12 --no-update-check 11 --no-update-check
13 --num-threads=\${GALAXY_SLOTS:-4} 12 --num-threads=\${GALAXY_SLOTS:-4}
14 ## Set advanced SE data parameters? 13 ## Set advanced SE data parameters?
15 #if $additional.sAdditional == "Yes": 14 #if $additional.sAdditional == "Yes":
49 #end if 48 #end if
50 ## Inputs. 49 ## Inputs.
51 '$gtf_input' 50 '$gtf_input'
52 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) 51 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
53 '$samplestring' 52 '$samplestring'
54 </command> 53 ]]></command>
55 <inputs> 54 <inputs>
56 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" 55 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
57 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> 56 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>
58 57
59 <repeat name="samples" title="Replicate" min="1"> 58 <repeat name="samples" title="Replicate" min="1">