# HG changeset patch
# User yhoogstrate
# Date 1389279671 18000
# Node ID ad5d660ae693a77d4259a1d954d01b04290bd73f
# Parent  1d5057b31cd2e0777331c916dfc7af0e4687d2a8
Uploaded

diff -r 1d5057b31cd2 -r ad5d660ae693 edgeR_DGE.xml
--- a/edgeR_DGE.xml	Thu Jan 09 09:54:13 2014 -0500
+++ b/edgeR_DGE.xml	Thu Jan 09 10:01:11 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>
+	<command interpreter="bash">
 		<!--
 			The following script is written in the "Cheetah" language:
 			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
@@ -22,8 +22,8 @@
 			$output_BCVplot
 			$output_MAplot
 			smearPlot '
-			&gt; $output_R
-			2&gt; &gt;(grep -v 'Calculating library sizes' 1&gt;&amp;amp;2)
+			> $output_R
+			2> >(grep -v 'Calculating library sizes' 1>&2)
 	</command>
 	
 	<inputs>