Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 70:fb64bf85361d draft

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Uploaded
author yhoogstrate
date Tue, 30 Sep 2014 10:47:33 -0400
parents 1dc20e3e11df
children 46896caca6be
files edgeR_Differential_Gene_Expression.xml
diffstat 1 files changed, 51 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 09:23:17 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 10:47:33 2014 -0400
@@ -85,26 +85,50 @@
 			
 			2> stderr.txt ; 
 			
-			#if $output_format_images == "png":
-				echo "Converting PDF figures to PNG"
+			#if $output_format_images.value == "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" ;
+				#if $output_MDSplot:
+					#set $output_MDSplot_tmp = str($output_MDSplot)+".png"
+					
+					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 ; 
+					mv $output_BCVplot_tmp $output_BCVplot ; 
+				#end if
 				
-				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 ;
+				#if $output_MAplot:
+					#set $output_MAplot_tmp = str($output_MAplot)+".png"
+					
+					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 ; 
+					mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ; 
+				#end if
 				
-				mv "{$output_format_images}.png" $output_format_images ; 
-			#else:
-				echo "Format is already in $output_format_images"
+				#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 ;  
+					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 ; 
+					mv $output_heatmap_plot_tmp $output_heatmap_plot ; 
+				#end if
 			#end if
 			
 			grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
@@ -266,7 +290,8 @@
       pdf(output_MDSplot)
     } else if(output_format_images == "svg") {
       svg(output_MDSplot)
-    ##} else {
+    }
+    ## else {
     ##  png(output_MDSplot)
     ##}
     
@@ -287,7 +312,8 @@
       pdf(output_BCVplot)
     } else if(output_format_images == "svg") {
       svg(output_BCVplot)
-    ##} else {
+    }
+    ##else {
     ##  png(output_BCVplot)
     ##}
     
@@ -322,7 +348,8 @@
         pdf(output_MAplot)
       } else if(output_format_images == "svg") {
         svg(output_MAplot)
-      ##} else {
+      }
+      ##else {
       ##  png(output_MAplot)
       ##}
       
@@ -339,7 +366,8 @@
         pdf(output_PValue_distribution_plot)
       } else if(output_format_images == "svg") {
         svg(output_PValue_distribution_plot)
-      ##} else {
+      }
+      ##else {
       ##  png(output_PValue_distribution_plot)
       ##}
       
@@ -365,7 +393,8 @@
       pdf(output_heatmap_plot,width=10.5)
     } else if(output_format_images == "svg") {
       svg(output_heatmap_plot,width=10.5)
-    ##} else {
+    }
+    ## else {
     ##  png(output_heatmap_plot,width=10.5)
     ##}