# HG changeset patch
# User pravs
# Date 1529543394 14400
# Node ID 8e9428eca82c22a5bb544c4292278d0db106376b
# Parent  6bf0203ee17eb576977efcf0f3ab3f57709174fe
planemo upload

diff -r 6bf0203ee17e -r 8e9428eca82c protein_rna_correlation.r
--- a/protein_rna_correlation.r	Wed Jun 20 20:43:56 2018 -0400
+++ b/protein_rna_correlation.r	Wed Jun 20 21:09:54 2018 -0400
@@ -536,7 +536,8 @@
 #=============================================================================================================
 	cat("Generating Box and Density plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/AbundancePlot.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot, "png16m");
 	par(mfrow=c(2,2));
 	boxplot(proteome_df[,2], ylab="Abundance", main="Proteome abundance", cex.lab=1.5);
 	plot(density(proteome_df[,2]), xlab="Protein Abundance", ylab="Density", main="Proteome abundance", cex.lab=1.5);
@@ -554,7 +555,8 @@
 #=============================================================================================================
 	cat("Generating scatter plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/AbundancePlot_scatter.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m")
 	par(mfrow=c(1,1));
 	scatter.smooth(transcriptome_df[,2], proteome_df[,2], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);	
 	
@@ -636,25 +638,29 @@
 	file = htmloutfile, append = TRUE);
 
 	outplot = paste(outdir,"/PE_GE_lm_1.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 1, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_2.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 2, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_3.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 3, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_5.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 5, cex.lab=1.5);
 	dev.off();
@@ -705,7 +711,8 @@
 	
 	cat("Generating cooksd plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_lm_cooksd.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(cooksd, pch="*", cex=2, cex.lab=1.5,main="Influential Obs. by Cooks distance", ylab="Cook\'s distance", xlab="Observations")  # plot cooks distance
 	abline(h = 4*mean(cooksd, na.rm=T), col="red")  # add cutoff line
@@ -765,7 +772,8 @@
 	# Scatter plot
 	#=============================================================================================================
 	outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	scatter.smooth(PE_GE_data_no_outlier[,"GE_abundance"], PE_GE_data_no_outlier[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);	
 	
@@ -807,7 +815,8 @@
 	
 	cat("Generating heatmap plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_heatmap.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	#heatmap.2(as.matrix(PE_GE_data[,c("PE_abundance","GE_abundance")]), trace="none", cexCol=1, col=greenred(100),Colv=F, labCol=c("PE","GE"), scale="col");
 	my_palette <- colorRampPalette(c("green", "white", "red"))(299);
@@ -828,7 +837,8 @@
 	k1 = kmeans(PE_GE_data_kdata[,c("PE_abundance","GE_abundance")], 5);
 	cat("Generating kmeans plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_kmeans.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	scatter.smooth(PE_GE_data_kdata[,"GE_abundance"], PE_GE_data_kdata[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);
 	
diff -r 6bf0203ee17e -r 8e9428eca82c protein_rna_correlation.xml
--- a/protein_rna_correlation.xml	Wed Jun 20 20:43:56 2018 -0400
+++ b/protein_rna_correlation.xml	Wed Jun 20 21:09:54 2018 -0400
@@ -3,8 +3,7 @@
   <requirements>
     <requirement type="package" version="3.2.1">R</requirement>
     <requirement type="package" version="0.0.1">r-protrnacorr</requirement>
-    <requirement type="package" version="1.5.0">x11</requirement>
-    
+    <!--<requirement type="package" version="1.5.0">x11</requirement>-->
   </requirements>
   <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[protein_rna_correlation.r $pe_exp $ge_exp $pe_idcol $ge_idcol $pe_expcol $ge_expcol $pe_idtype $ge_idtype $organism_map $writeMapUnmap $doScale $html_file $html_file.files_path]]></command>
   <inputs>
diff -r 6bf0203ee17e -r 8e9428eca82c tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 20 20:43:56 2018 -0400
+++ b/tool_dependencies.xml	Wed Jun 20 21:09:54 2018 -0400
@@ -38,7 +38,7 @@
         Contains a tool dependency definition that downloads and installs protein rna correlation tool package for R library.
         </readme>
     </package>
-    <package name="x11" version="1.5.0">
-        <repository changeset_revision="2ecb3f1f8fbb" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
+    <!--<package name="x11" version="1.5.0">
+            <repository changeset_revision="2ecb3f1f8fbb" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>-->
 </tool_dependency>