# HG changeset patch
# User jeremy goecks <jeremy.goecks@emory.edu>
# Date 1382454182 14400
# Node ID 2d6a90609943261c47f935418368d30017db0502
# Parent  60a52f8460a1d32f4403355d1085c7fde1d5429b
Fix wrapper bugs: (a) do not try update check and (b) allow spaces in labels.

diff -r 60a52f8460a1 -r 2d6a90609943 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed Oct 09 12:49:03 2013 -0400
+++ b/cuffdiff_wrapper.xml	Tue Oct 22 11:03:02 2013 -0400
@@ -7,6 +7,7 @@
     <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
     <command>
         cuffdiff
+            --no-update-check
             --FDR=$fdr
             --num-threads="4"
             --min-alignment-count=$min_alignment_count
@@ -36,7 +37,7 @@
                 #end if
             #end if
 
-            #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] )
+            #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
             --labels $labels
 
             ## Inputs.