--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsmap_meth_caller.sh	Mon Dec 03 02:42:04 2012 -0500
@@ -0,0 +1,32 @@
+#!/bin/bash
+#
+# Galaxy wrapper for BSMAP Methylation Caller
+#
+
+set -e
+
+#get parameters
+
+until [ $# -eq 0 ]
+do
+	case $1 in
+		input=*)
+			input=${1#input=}
+			;;
+		method=*)
+			method=${1#method=}
+			;;
+		output=*)
+			output=${1#output=}
+			;;
+		tempdir=*)
+			tempdir=${1#tempdir=}
+			;;
+		ref=*)
+			ref=${1#ref=}
+			;;
+	esac
+	shift
+done
+
+methratio.py -o $output -d $ref -q $input
\ No newline at end of file