# HG changeset patch
# User yhoogstrate
# Date 1408966612 14400
# Node ID 8c63794c3d3efa1e86e147da478e5a38b0ab9baf
# Parent  cef8f2a174fca6ce640065c9153221af01d65dc5
Uploaded

diff -r cef8f2a174fc -r 8c63794c3d3e edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Thu Jun 19 05:15:23 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Mon Aug 25 07:36:52 2014 -0400
@@ -72,7 +72,9 @@
 			#else:
 				/dev/null
 			#end if
-			 '
+			
+			$output_format_images
+			'
 			#if $output_R:
 				> $output_R 
 			#else:
@@ -116,6 +118,12 @@
 			<option value="make_output_R_stdout">R stdout</option>
 			<option value="make_output_RData_obj">R Data object</option>
 		</param>
+		
+		<param name="output_format_images" type="select" label="Output format of images" display="radio">
+			<option value="png">Portable network graphics (.png)</option>
+			<option value="pdf">Portable document format (.pdf)</option>
+			<option value="svg">Scalable vector graphics (.svg)</option>
+		</param>
 	</inputs>
 	
 	<configfiles>
@@ -146,6 +154,7 @@
 output_hierarchical_clustering_plot = args[13]
 output_heatmap_plot                 = args[14]
 output_RData_obj                    = args[15]
+output_format_images                = args[16]
 
 
 library(edgeR)
@@ -229,7 +238,16 @@
     points &lt;- plotMDS.DGEList(dge,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
     dev.off()# Kill it
     
-    pdf(output_MDSplot)
+    if(output_format_images == "pdf") {
+      capabilities()
+      ##x11()
+      pdf(output_MDSplot)
+    } else if(output_format_images == "svg") {
+      svg(output_MDSplot)
+    } else {
+      png(output_MDSplot)
+    }
+    
     diff_x &lt;- abs(max(points\$x)-min(points\$x))
     diff_y &lt;-(max(points\$y)-min(points\$y))
     plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR MDS Plot",type="n", xlab="BCV distance 1", ylab="BCV distance 2")
@@ -324,27 +342,27 @@
 			<filter>outputs and ("make_output_raw_counts" in outputs)</filter>
 		</data>
 		
-		<data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
+		<data format="${output_format_images}" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
 			<filter>outputs and ("make_output_MDSplot" in outputs)</filter>
 		</data>
 		
-		<data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
+		<data format="${output_format_images}" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
 			<filter>outputs and ("make_output_BCVplot" in outputs)</filter>
 		</data>
 		
-		<data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
+		<data format="${output_format_images}" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
 			<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}: ${design_matrix.name} - P-Value distribution">
+		<data format="${output_format_images}" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
 			<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}: ${design_matrix.name} - Hierarchical custering">
+		<data format="${output_format_images}" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
 			<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}: ${design_matrix.name} - Heatmap">
+		<data format="${output_format_images}" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
 			<filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
 		</data>