# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1374065919 18000
# Node ID 4597c429b6fb6f9dbb0dedc00b7ab06d345249b4
# Parent  e132e60f95b153de9bcce00d6f60bd172d39781d
Return nonzero exit code from cuffdiff_wrapper.py on error

diff -r e132e60f95b1 -r 4597c429b6fb cuffdiff_wrapper.py
--- 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 ):
diff -r e132e60f95b1 -r 4597c429b6fb cuffdiff_wrapper.xml
--- 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>