# HG changeset patch
# User yhoogstrate
# Date 1389283592 18000
# Node ID d86d9d498dc7d1b4e3c22d3d0d577cf1f613f6c7
# Parent  ad5d660ae693a77d4259a1d954d01b04290bd73f
Uploaded

diff -r ad5d660ae693 -r d86d9d498dc7 edgeR_DGE.xml
--- a/edgeR_DGE.xml	Thu Jan 09 10:01:11 2014 -0500
+++ b/edgeR_DGE.xml	Thu Jan 09 11:06:32 2014 -0500
@@ -2,7 +2,7 @@
 <tool id="edger_dge" name="edgeR Differential GeneExpression Analysis">
 	<description>RNA-Seq expression analysis using edgeR (R package)</description>
 	
-	<command interpreter="bash">
+	<command>
 		<!--
 			The following script is written in the "Cheetah" language:
 			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
@@ -23,7 +23,9 @@
 			$output_MAplot
 			smearPlot '
 			> $output_R
-			2> >(grep -v 'Calculating library sizes' 1>&2)
+			2> stderr.txt ;
+			grep -v 'Calculating library sizes from column' stderr.txt 1>&2
+	
 	</command>
 	
 	<inputs>