--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsmap_wrapper.sh	Thu Nov 29 10:10:16 2012 -0500
@@ -0,0 +1,133 @@
+#!/bin/bash
+#
+# Galaxy wrapper for BSMAP
+# Written by Eugen Eirich @ Institute for Molecular Biology Mainz
+#
+
+set -e
+
+#get parameters
+
+until [ $# -eq 0 ]
+do
+	case $1 in
+		ref=*)
+			ref=${1#ref=}
+			;;
+		library=*)
+			library=${1#library=}
+			;;
+		unpaired=*)
+			unpaired=${1#unpaired=}
+			;;
+		mapped=*)
+			mapped=${1#mapped=}
+			;;
+		fullparam=*)
+			fullparam=${1#fullparam=}
+			;;
+		mate1=*)
+			mate1=${1#mate1=}
+			;;
+		mate2=*)
+			mate2=${1#mate2=}
+			;;
+		qual=*)
+			qual="-z ${1#qual=}"
+			;;
+		threshold=*)
+			threshold="-q ${1#threshold=}"
+			;;
+		lowqual=*)
+			lowqual="-f ${1#lowqual=}"
+			;;
+		adapter=*)
+			adapter=${1#adapter=}
+			;;
+		firstn=*)
+			firstn="-L ${1#firstn=}"
+			;;
+		repeat_reads=*)
+			repeat_reads="-r ${1#repeat_reads=}"
+			;;
+		seed_size=*)
+			seed_size="-s ${1#seed_size=}"
+			;;
+		mismatch=*)
+			mismatch="-v ${1#mismatch=}"
+			;;
+		equal_best=*)
+			equal_best="-w ${1#equal_best=}"
+			;;
+		start=*)
+			start="-B ${1#start=}"
+			;;
+		end=*)
+			end="-E ${1#end=}"
+			;;
+		index_interval=*)
+			index_interval="-I ${1#index_interval=}"
+			;;
+		seed_random=*)
+			seed_random=${1#seed_random=}
+			;;
+		rrbs=*)
+			rrbs=${1#rrbs=}
+			;;
+		mode=*)
+			mode="-n ${1#mode=}"
+			;;
+		align_info=*)
+			align_info=${1#align_info=}
+			;;
+		maxinsert=*)
+			maxinsert="-x ${1#maxinsert=}"
+			;;
+		mininsert=*)
+			mininsert="-m ${1#mininsert=}"
+			;;
+		summary=*)
+			summary=${1#summary=}
+			;;
+	esac
+	shift
+done
+
+
+if [ "$rrbs" != "" ]
+then
+  rrbs="-D $rrbs"
+fi
+
+if [ "$align_info" != "" ]
+then
+  align_info="-M $align_info"
+fi
+
+if [ "$adapter" != "" ]
+then
+  adapter="-A $adapter"
+fi
+
+if [ "$seed_random" != "" ]
+then
+  seed_random="-S $seed_random"
+fi
+
+
+if [ "$library" == "single" ]
+then
+    if [ "$fullparam" == 'false' ]
+    then      
+      bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 > $summary
+    else
+      bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode  > $summary
+    fi
+else
+    if [ "$fullparam" == 'false' ]
+    then
+      bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4  > $summary
+    else
+      bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode $maxinsert $mininsert   > $summary
+    fi
+fi