# HG changeset patch
# User yhoogstrate
# Date 1402665102 14400
# Node ID b89788eead3ccca76978b34e8e789cf684b943f9
# Parent  7fc17dc8377701e9c0071b4c2912c3fa7cea850f
Uploaded

diff -r 7fc17dc83777 -r b89788eead3c edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Wed Jun 04 07:08:26 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Fri Jun 13 09:11:42 2014 -0400
@@ -79,9 +79,20 @@
 				> /dev/null
 			#end if
 			
-			2> stderr.txt
-			;
-			grep -v 'Calculating library sizes from column' stderr.txt 1>&2
+			2> stderr.txt ; 
+			
+			grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			
+			## Locale error messages:
+			grep -v 'During startup - Warning messages' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_TIME failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_MONETARY failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_PAPER failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_MEASUREMENT failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_CTYPE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
+			
+			cat stderr.txt >&2
 	
 	</command>
 	
@@ -306,43 +317,43 @@
 	</configfiles>
 	
 	<outputs>
-		<data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differtially expressed genes" />
+		<data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
 		<data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
 		
 		<data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
-			<filter>("make_output_raw_counts" in outputs)</filter>
+			<filter>outputs and ("make_output_raw_counts" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
-			<filter>("make_output_MDSplot" in outputs)</filter>
+			<filter>outputs and ("make_output_MDSplot" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
-			<filter>("make_output_BCVplot" in outputs)</filter>
+			<filter>outputs and ("make_output_BCVplot" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
-			<filter>("make_output_MAplot" in outputs)</filter>
+			<filter>outputs and ("make_output_MAplot" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
-			<filter>("make_output_PValue_distribution_plot" in outputs)</filter>
+			<filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
-			<filter>("make_output_hierarchical_clustering_plot" in outputs)</filter>
+			<filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
 		</data>
 		
 		<data format="pdf" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
-			<filter>("make_output_heatmap_plot" in outputs)</filter>
+			<filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
 		</data>
 		
 		<data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
-			<filter>("make_output_RData_obj" in outputs)</filter>
+			<filter>outputs and ("make_output_RData_obj" in outputs)</filter>
 		</data>
 		
 		<data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
-			<filter>("make_output_R_stdout" in outputs)</filter>
+			<filter>outputs and ("make_output_R_stdout" in outputs)</filter>
 		</data>
 	</outputs>