--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idrPlotWrapper.sh	Thu Jan 17 15:59:22 2013 -0500
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# idrPlotWrapper.sh
+# OICR: Kar Ming Chu
+# July 2012
+
+# BASH wrapper for batch-consistency-plot.r (part of the IDR package)
+# For use with Galaxy 
+
+# Usage of batch-consistency-plot.r: Rscript batch-consistency-plot-merged.r [npairs] [output.dir] [input.file.prefix 1, 2, 3 ...]
+#	npairs - will be a constant, since Galaxy requires explicit control over input and output files
+
+# Usage of THIS SCRIPT: ./idrPlotWrapper.sh em uri outputfile
+#	em - em.sav file provided by Galaxy
+#	uri - uri.sav file provided by Galaxy
+#	outputfile - output file name specified by Galaxy
+
+main() {
+	EM="${1}" 		# absolute file path to em.sav file, provided by Galaxy
+	URI="${2}"		# absolute file parth to uri.sav file, provided by Galaxy
+	OUTFILE="${3}"		# name of desired output file
+
+	cp "${EM}" ./idrPlot-em.sav	# cp to this directory and rename so they can be found by idrPlot
+	cp "${URI}" ./idrPlot-uri.sav
+	
+	Rscript /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/idr/batch-consistency-plot.r 1 ./idrPlot idrPlot
+
+	# convert post script to pdf file
+ 	ps2pdf ./idrPlot-plot.ps ./idrPlot-plot.pdf
+
+	# rename to output file name
+	mv ./idrPlot-plot.pdf "${OUTFILE}"
+
+	# clean up
+	rm idrPlot-em.sav
+	rm idrPlot-uri.sav
+}
+
+main "${@}"