--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parsewig.sh	Mon Dec 03 02:53:01 2012 -0500
@@ -0,0 +1,51 @@
+#!/bin/bash
+#
+# Galaxy wrapper for BSMAP Methylation Caller
+#
+
+set -e
+
+
+#get parameters
+
+until [ $# -eq 0 ]
+do
+	case $1 in
+		input=*)
+			input=${1#input=}
+			;;
+		extract=*)
+			extract=${1#extract=}
+			;;
+		context=*)
+			context=${1#context=}
+			;;
+		depth=*)
+			depth="cutoff=${1#depth=}"
+			;;
+		cov_out=*)
+			cov_out=${1#cov_out=}
+			;;
+		meth_out=*)
+			meth_out=${1#meth_out=}
+			;;
+	esac
+	shift
+done
+
+case $extract in
+      c)
+	output="-cov_out=$cov_out";;
+      m)
+	output="-meth_out=$meth_out";;
+      b)
+	output="-meth_out=$meth_out -cov_out=$cov_out";;
+esac
+
+if [ "$context" != "" ] 
+then
+    context="-context=$context"
+fi
+
+
+perl ~/dependencies/wig-parser/wiggle_extractor.pl -e $extract $context $output $input 2>&1>/dev/null
\ No newline at end of file