# HG changeset patch
# User yhoogstrate
# Date 1389278717 18000
# Node ID 199695284f80af8b9b4bd27c28b1d175c08a1a7b
# Parent  8a96492419643103a41393a4fec7b7d0fecf13c1
Uploaded

diff -r 8a9649241964 -r 199695284f80 edgeR_DGE.xml
--- a/edgeR_DGE.xml	Thu Jan 09 09:35:19 2014 -0500
+++ b/edgeR_DGE.xml	Thu Jan 09 09:45:17 2014 -0500
@@ -22,8 +22,8 @@
 			$output_BCVplot
 			$output_MAplot
 			smearPlot '
-			> $output_R
-			2> >(grep -v 'Calculating' | grep -v 'library' | grep -v 'sizes'  1>&2)
+			> $output_R
+			2> >(grep -v Calculating \| grep -v \| grep -v sizes 1>&2 )
 	</command>
 	
 	<inputs>
@@ -32,13 +32,13 @@
 		<param name="contrast" type="text" label="Contrast (biological question)" help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info." />
 		
 		<param name="qc" type="select" label="Quality control reports">
-			<option value="true">Yes</option>
-			<option value="false" selected="true">No</option>
+			<option value="true" selected="true">Yes</option>
+			<option value="false">No</option>
 		</param>
 		
 		<param name="debug" type="select" label="R Debug output">
-			<option value="true" selected="true"> Yes</option>
-			<option value="false">No</option>
+			<option value="true"> Yes</option>
+			<option value="false" selected="true">No</option>
 		</param>
 	</inputs>