Mercurial > repos > jjohnson > cummerbund
changeset 13:4597c429b6fb
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 | e132e60f95b1 |
| children | d10befb0867a |
| files | cuffdiff_wrapper.py cuffdiff_wrapper.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/cuffdiff_wrapper.py Sun Oct 21 18:17:51 2012 -0500 +++ b/cuffdiff_wrapper.py Wed Jul 17 07:58:39 2013 -0500 @@ -33,7 +33,7 @@ def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) - sys.exit() + sys.exit(1) # Copied from sam_to_bam.py: def check_seq_file( dbkey, cached_seqs_pointer_file ):
--- a/cuffdiff_wrapper.xml Sun Oct 21 18:17:51 2012 -0500 +++ b/cuffdiff_wrapper.xml Wed Jul 17 07:58:39 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.0.6"> +<tool id="cuffdiff_cummerbund" name="Cuffdiff" version="0.0.6"> <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 --> <description>find significant changes in transcript expression, splicing, and promoter use</description> <requirements> @@ -114,7 +114,7 @@ </command> <inputs> - <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> + <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."/> <conditional name="group_analysis"> <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."> <option value="No">No</option>