# HG changeset patch
# User yhoogstrate
# Date 1412083397 14400
# Node ID 1dc20e3e11df9b6072b05e61923f4e384fc586bf
# Parent  718bb1dd0b8a2db6b3bdd3b512c385aad9cbcbd2
Uploaded

diff -r 718bb1dd0b8a -r 1dc20e3e11df edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 09:09:29 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 09:23:17 2014 -0400
@@ -86,8 +86,25 @@
 			2> stderr.txt ; 
 			
 			#if $output_format_images == "png":
-				convert $output_format_images "{$output_format_images}.png" ; 
+				echo "Converting PDF figures to PNG"
+				
+				convert $output_MDSplot "{$output_MDSplot}.png" ;
+				convert $output_BCVplot "{$output_BCVplot}.png" ;
+				convert $output_MAplot "{$output_MAplot}.png" ;
+				convert $output_PValue_distribution_plot "{$output_PValue_distribution_plot}.png" ;
+				convert $output_hierarchical_clustering_plot "{$output_hierarchical_clustering_plot}.png" ;
+				convert $output_heatmap_plot "{$output_heatmap_plot}.png" ;
+				
+				mv "{$output_MDSplot}.png" $output_MDSplot ;
+				mv "{$output_BCVplot}.png" $output_BCVplot ;
+				mv "{$output_MAplot}.png" $output_MAplot ;
+				mv "{$output_PValue_distribution_plot}.png" $output_PValue_distribution_plot ;
+				mv "{$output_hierarchical_clustering_plot}.png" $output_hierarchical_clustering_plot ;
+				mv "{$output_heatmap_plot}.png" $output_heatmap_plot ;
+				
 				mv "{$output_format_images}.png" $output_format_images ; 
+			#else:
+				echo "Format is already in $output_format_images"
 			#end if
 			
 			grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;