Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 90:f87938c392bf draft

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Hardcoded the png: suffix for gm convert, to ensure conversion to png
author yhoogstrate
date Wed, 28 Jan 2015 09:43:55 -0500
parents 875f080136b6
children c81da57fff20
files edgeR_Differential_Gene_Expression.xml
diffstat 1 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Wed Jan 28 09:22:54 2015 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Jan 28 09:43:55 2015 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.b">
+<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.c">
 	<description>RNA-Seq gene expression analysis using edgeR (R package)</description>
 	
 	<requirements>
@@ -100,49 +100,49 @@
 				#if $output_MDSplot_logFC:
 					#set $output_MDSplot_logFC_tmp = str($output_MDSplot_logFC)+".png"
 					
-					gm convert $output_MDSplot_logFC $output_MDSplot_logFC_tmp ; 
+					gm convert $output_MDSplot_logFC png:$output_MDSplot_logFC_tmp ; 
 					mv $output_MDSplot_logFC_tmp $output_MDSplot_logFC ; 
 				#end if
 				
 				#if $output_MDSplot_bcv:
 					#set $output_MDSplot_bcv_tmp = str($output_MDSplot_bcv)+".png"
 					
-					gm convert $output_MDSplot_bcv $output_MDSplot_bcv_tmp ; 
+					gm convert $output_MDSplot_bcv png:$output_MDSplot_bcv_tmp ; 
 					mv $output_MDSplot_bcv_tmp $output_MDSplot_bcv ; 
 				#end if
 				
 				#if $output_BCVplot:
 					#set $output_BCVplot_tmp = str($output_BCVplot)+".png"
 					
-					gm convert $output_BCVplot $output_BCVplot_tmp ; 
+					gm convert $output_BCVplot png:$output_BCVplot_tmp ; 
 					mv $output_BCVplot_tmp $output_BCVplot ; 
 				#end if
 				
 				#if $output_MAplot:
 					#set $output_MAplot_tmp = str($output_MAplot)+".png"
 					
-					gm convert $output_MAplot $output_MAplot_tmp ; 
+					gm convert $output_MAplot png:$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"
 					
-					gm convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 
+					gm convert $output_PValue_distribution_plot png:$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"
 					
-					gm convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;  
+					gm convert $output_hierarchical_clustering_plot png:$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"
 					
-					gm convert $output_heatmap_plot $output_heatmap_plot_tmp ; 
+					gm convert $output_heatmap_plot png:$output_heatmap_plot_tmp ; 
 					mv $output_heatmap_plot_tmp $output_heatmap_plot ; 
 				#end if
 			#end if