Mercurial > repos > lparsons > cutadapt

diff cutadapt.xml @ 4:0a872e59164c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 19:33:40 -0400
parents 7ed26fc9fa8a
children 1dada50cca8a
line wrap: on
line diff
--- a/cutadapt.xml	Wed May 25 18:54:09 2011 -0400
+++ b/cutadapt.xml	Wed May 25 19:33:40 2011 -0400
@@ -4,7 +4,7 @@
 		<requirement type="python-module">cutadapt</requirement>
 	</requirements>
 
-	<command>cutadapt 
+	<command interpreter="sh">discard_stderr_wrapper.sh cutadapt
 		#if $input.extension.startswith( "fastq"):
 		--format=fastq
 		#else
@@ -30,7 +30,7 @@
 		#end if
 		'$input'
 		--output='$output' 
-		2> $report
+		> $report
 	</command>
 	<inputs>
 		<param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>