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comparison cuffdiff_wrapper.xml @ 13:4597c429b6fb

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Return nonzero exit code from cuffdiff_wrapper.py on error
author Jim Johnson <jj@umn.edu>
date Wed, 17 Jul 2013 07:58:39 -0500
parents 56bdf6d4ac9c
children d10befb0867a
comparison
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12:e132e60f95b1 13:4597c429b6fb
1 <tool id="cuffdiff" name="Cuffdiff" version="0.0.6"> 1 <tool id="cuffdiff_cummerbund" name="Cuffdiff" version="0.0.6">
2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 --> 2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
3 <description>find significant changes in transcript expression, splicing, and promoter use</description> 3 <description>find significant changes in transcript expression, splicing, and promoter use</description>
4 <requirements> 4 <requirements>
5 <requirement type="package">cufflinks</requirement> 5 <requirement type="package">cufflinks</requirement>
6 </requirements> 6 </requirements>
112 #end for 112 #end for
113 #end if 113 #end if
114 114
115 </command> 115 </command>
116 <inputs> 116 <inputs>
117 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> 117 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
118 <conditional name="group_analysis"> 118 <conditional name="group_analysis">
119 <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."> 119 <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group.">
120 <option value="No">No</option> 120 <option value="No">No</option>
121 <option value="Yes">Yes</option> 121 <option value="Yes">Yes</option>
122 </param> 122 </param>