Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 91:c81da57fff20 draft

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Uploaded
author yhoogstrate
date Mon, 09 Mar 2015 08:35:13 -0400
parents f87938c392bf
children 86c3aaa205b5
files edgeR_Differential_Gene_Expression.xml tool_dependencies.xml
diffstat 2 files changed, 42 insertions(+), 92 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Wed Jan 28 09:43:55 2015 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Mon Mar 09 08:35:13 2015 -0400
@@ -1,13 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.c">
+<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.d">
 	<description>RNA-Seq gene expression analysis using edgeR (R package)</description>
 	
 	<requirements>
-		<!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
-		<!--<requirement type="package" version="3.1.0">R</requirement>-->
 		<requirement type="package" version="3.0.3">R</requirement>
 		<requirement type="package" version="latest">biocLite_edgeR_limma</requirement>
-		<requirement type="package" version="1.3.18">graphicsmagick</requirement>
 	</requirements>
 	
 	<version_command>R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null</version_command>
@@ -94,59 +91,6 @@
 			
 			2> stderr.txt ; 
 			
-			#if $output_format_images.value == "png":
-				echo "Converting PDF figures to PNG" ; 
-				
-				#if $output_MDSplot_logFC:
-					#set $output_MDSplot_logFC_tmp = str($output_MDSplot_logFC)+".png"
-					
-					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 $output_MDSplot_bcv png:$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 $output_BCVplot png:$output_BCVplot_tmp ; 
-					mv $output_BCVplot_tmp $output_BCVplot ; 
-				#end if
-				
-				#if $output_MAplot:
-					#set $output_MAplot_tmp = str($output_MAplot)+".png"
-					
-					gm convert $output_MAplot png:$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 $output_PValue_distribution_plot png:$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 $output_hierarchical_clustering_plot png:$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 $output_heatmap_plot png:$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 ; 
 			
 			## Locale error messages:
@@ -306,15 +250,17 @@
     points &lt;- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
     dev.off()# Kill it
     
-    if(output_format_images == "pdf" || output_format_images == "png") {
+    if(output_format_images == "pdf") {
       pdf(output_MDSplot_logFC,height=14,width=14)
     } else if(output_format_images == "svg") {
       svg(output_MDSplot_logFC,height=14,width=14)
+    } else {
+      ## png(output_MDSplot_logFC)
+      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+      
+      bitmap(output_MDSplot_logFC,type="png16m",height=14,width=14)
     }
-    ## else {
-    ##  png(output_MDSplot_logFC)
-    ##}
-    ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings
+    
     
     diff_x &lt;- abs(max(points\$x)-min(points\$x))
     diff_y &lt;-(max(points\$y)-min(points\$y))
@@ -332,15 +278,16 @@
     points &lt;- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
     dev.off()# Kill it
     
-    if(output_format_images == "pdf" || output_format_images == "png") {
+    if(output_format_images == "pdf") {
       pdf(output_MDSplot_bcv,height=14,width=14)
     } else if(output_format_images == "svg") {
       svg(output_MDSplot_bcv,height=14,width=14)
+    } else {
+      ## png(output_MDSplot_bcv)
+      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+      
+      bitmap(output_MDSplot_bcv,type="png16m",height=14,width=14)
     }
-    ## else {
-    ##  png(output_MDSplot_bcv)
-    ##}
-    ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings
     
     diff_x &lt;- abs(max(points\$x)-min(points\$x))
     diff_y &lt;-(max(points\$y)-min(points\$y))
@@ -356,14 +303,16 @@
   if(output_BCVplot != "/dev/null") {
     write("Creating Biological coefficient of variation plot",stdout())
     
-    if(output_format_images == "pdf" || output_format_images == "png") {
+    if(output_format_images == "pdf") {
       pdf(output_BCVplot)
     } else if(output_format_images == "svg") {
       svg(output_BCVplot)
+    } else {
+      ## png(output_BCVplot)
+      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+      
+      bitmap(output_BCVplot,type="png16m")
     }
-    ##else {
-    ##  png(output_BCVplot)
-    ##}
     
     plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
     dev.off()
@@ -392,14 +341,16 @@
     if(output_MAplot != "/dev/null") {
       write("Creating MA plot...",stdout())
       
-      if(output_format_images == "pdf" || output_format_images == "png") {
+      if(output_format_images == "pdf") {
         pdf(output_MAplot)
       } else if(output_format_images == "svg") {
         svg(output_MAplot)
+      } else {
+        ## png(output_MAplot)
+        ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+        
+        bitmap(output_MAplot,type="png16m")
       }
-      ##else {
-      ##  png(output_MAplot)
-      ##}
       
       with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
       with(subset(etable, FDR &lt; fdr), points(logCPM, logFC, pch=20, col="red"))
@@ -410,14 +361,16 @@
     if(output_PValue_distribution_plot != "/dev/null") {
       write("Creating P-value distribution plot...",stdout())
       
-      if(output_format_images == "pdf" || output_format_images == "png") {
-        pdf(output_PValue_distribution_plot)
+      if(output_format_images == "pdf") {
+        pdf(output_PValue_distribution_plot,width=14,height=14)
       } else if(output_format_images == "svg") {
-        svg(output_PValue_distribution_plot)
+        svg(output_PValue_distribution_plot,width=14,height=14)
+      } else {
+        ## png(output_PValue_distribution_plot)
+        ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+        
+        bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14)
       }
-      ##else {
-      ##  png(output_PValue_distribution_plot)
-      ##}
       
       expressed_genes &lt;- subset(etable, PValue &lt; 0.99)
       h &lt;- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (&lt; 0.99)")
@@ -437,14 +390,16 @@
   
   if(output_heatmap_plot != "/dev/null") {
     
-    if(output_format_images == "pdf" || output_format_images == "png") {
+    if(output_format_images == "pdf") {
       pdf(output_heatmap_plot,width=10.5)
     } else if(output_format_images == "svg") {
       svg(output_heatmap_plot,width=10.5)
+    } else {
+      ## png(output_heatmap_plot)
+      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+      
+      bitmap(output_heatmap_plot,type="png16m",width=10.5)
     }
-    ## else {
-    ##  png(output_heatmap_plot,width=10.5)
-    ##}
     
     etable2 &lt;- topTags(lrt, n=100)\$table
     order &lt;- rownames(etable2)
--- a/tool_dependencies.xml	Wed Jan 28 09:43:55 2015 -0500
+++ b/tool_dependencies.xml	Mon Mar 09 08:35:13 2015 -0400
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	<package name="R" version="3.0.3">
-		<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+		<repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 	
 	<package name="biocLite_edgeR_limma" version="latest">
 		<install version="1.0"> 
 			<actions>
 				<action type="set_environment_for_install">
-					<repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+					<repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
 						<package name="R" version="3.0.3" />
 					</repository>
 					
@@ -28,11 +28,6 @@
 	   </readme>
 	</package>
 	
-	<!-- instead of using "convert", make use of "gm convert" -->
-	<package name="graphicsmagick" version="1.3.18">
-		<repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-	
 	<package name="design_matrix_creator" version="1.0.0">
 		<install version="1.0">
 			<actions>