# HG changeset patch
# User yhoogstrate
# Date 1412090668 14400
# Node ID e75afef75c13af5cb252f898f22353a685a7480b
# Parent  46896caca6bee3e2e8cb393fe64657b00b3ce3a0
Uploaded

diff -r 46896caca6be -r e75afef75c13 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 11:24:21 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 11:24:28 2014 -0400
@@ -7,6 +7,9 @@
 		<!--<requirement type="package" version="3.1.0">R</requirement>-->
 		<requirement type="package" version="3.0.3">R</requirement>
 		<requirement type="package" version="latest">package_biocLite_edgeR_limma</requirement>
+		<requirement type="package" version="1.3.18">graphicsmagick</requirement>
+	</package>
+	-->
 	</requirements>
 	
 	<command>
@@ -91,42 +94,42 @@
 				#if $output_MDSplot:
 					#set $output_MDSplot_tmp = str($output_MDSplot)+".png"
 					
-					convert $output_MDSplot $output_MDSplot_tmp ; 
+					gm convert $output_MDSplot $output_MDSplot_tmp ; 
 					mv $output_MDSplot_tmp $output_MDSplot ; 
 				#end if
 				
 				#if $output_BCVplot:
 					#set $output_BCVplot_tmp = str($output_BCVplot)+".png"
 					
-					convert $output_BCVplot $output_BCVplot_tmp ; 
+					gm convert $output_BCVplot $output_BCVplot_tmp ; 
 					mv $output_BCVplot_tmp $output_BCVplot ; 
 				#end if
 				
 				#if $output_MAplot:
 					#set $output_MAplot_tmp = str($output_MAplot)+".png"
 					
-					convert $output_MAplot $output_MAplot_tmp ; 
+					gm convert $output_MAplot $output_MAplot_tmp ; 
 					mv $output_MAplot_tmp $output_MAplot ; 
 				#end if
 				
 				#if $output_PValue_distribution_plot:
 					#set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
 					
-					convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 
+					gm convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 
 					mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ; 
 				#end if
 				
 				#if $output_hierarchical_clustering_plot:
 					#set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
 					
-					convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;  
+					gm convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;  
 					mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ; 
 				#end if
 				
 				#if $output_heatmap_plot:
 					#set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
 					
-					convert $output_heatmap_plot $output_heatmap_plot_tmp ; 
+					gm convert $output_heatmap_plot $output_heatmap_plot_tmp ; 
 					mv $output_heatmap_plot_tmp $output_heatmap_plot ; 
 				#end if
 			#end if
@@ -143,7 +146,7 @@
 			grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
 			
 			cat stderr.txt >&amp;2
-	
+			
 	</command>
 	
 	<inputs>