# HG changeset patch
# User jbrayet
# Date 1454684875 18000
# Node ID 173b23aa37da8ad963491e7cbfec904a1d7d20aa
# Parent  b8e8b0a4b41c4b27948a3c7104973697ba9a8017
Uploaded

diff -r b8e8b0a4b41c -r 173b23aa37da ChIPQC_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ChIPQC_wrapper.sh	Fri Feb 05 10:07:55 2016 -0500
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+
+while getopts "f:c:m:o:s:u:p:" optionName; do
+case "$optionName" in
+
+f) CHIPFILE="$OPTARG";;
+c) CONTROLFILE="$OPTARG";;
+m) MINVAL="$OPTARG";;
+s) MAXVAL="$OPTARG";;
+o) OUTPUT="$OPTARG";;
+u) OUTSTAT="$OPTARG";;
+p) PDF="$OPTARG";;
+
+esac
+done
+
+local_path=/usr/bin/ChIPQC
+R_PATH='Rscript --slave '
+
+echo "$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF"
+$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF
+