# HG changeset patch
# User eugen
# Date 1345035186 14400
# Node ID ee3bd6ad3958a0042cc583ee19ce0fc986a93683
# Parent  1d29aebf96aea4ca90b38ec127471bd43ce7e5e9
Uploaded

diff -r 1d29aebf96ae -r ee3bd6ad3958 bismark_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_wrapper.sh	Wed Aug 15 08:53:06 2012 -0400
@@ -0,0 +1,112 @@
+#!/bin/bash
+#
+# Galaxy wrapper for Bismark
+#
+
+set -e
+
+
+#get parameters
+
+until [ $# -eq 0 ]
+do
+	case $1 in
+		ref=*)
+			ref=${1#ref=}
+			;;
+		library=*)
+			library=${1#library=}
+			;;
+		fullparam=*)
+			fullparam=${1#fullparam=}
+			;;
+		mate1=*)
+			mate1=${1#mate1=}
+			;;
+		mate2=*)
+			mate2=${1#mate2=}
+			;;
+		qual=*)
+			qual=${1#qual=}
+			;;
+		seedmms=*)
+			seedmms="--seedmms ${1#seedmms=}"
+			;;
+		seedlen=*)
+			seedlen="--seedlen ${1#seedlen=}"
+			;;
+		maqerr=*)
+			maqerr="--maqerr ${1#maqerr=}"
+			;;
+		directional=*)
+			directional=${1#directional=}
+			;;
+		header=*)
+			header=${1#header=}
+			;;
+		minins=*)
+			minins="--minins ${1#minins=}"
+			;;
+		maxins=*)
+			maxins="--maxins ${1#maxins=}"
+			;;
+		mapped=*)
+			mapped=${1#mapped=}
+			;;
+		summary=*)
+			summary=${1#summary=}
+			;;
+		tempdir=*)
+			tempdir=${1#tempdir=}
+			;;
+	esac
+	shift
+done
+
+
+if [ "$library" == "single" ]
+then
+    if [ "$fullparam" == 'false' ]
+    then      
+      bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref $mate1  2>&1 > /dev/null
+    else
+      bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $ref $mate1  2>&1 > /dev/null
+    fi
+else
+    if [ "$fullparam" == 'false' ]
+    then
+      bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null
+    else
+      bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $minins $maxins $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null
+    fi
+fi
+
+
+#call bismark. output in temp-directory (files_path)
+
+
+#parse the filename of the input -> same as output
+IFS="/"
+set - $mate1
+outfile=${*:$#:1}
+
+#sort the mapped reads by chromosome
+#sort -k 3,3 -k 4,4n "$tempdir/${outfile}_bismark_pe.sam" > "$tempdir/${outfile}_bismark_pe_sorted.sam"
+
+#copy resultfiles back into galaxy
+#cp "$tempdir/${outfile}_bismark_sorted.sam" "$mapped"
+if [ "$library" == "single" ]
+then
+    cp "$tempdir/${outfile}_bismark.sam" "$mapped"
+    cp "$tempdir/${outfile}_Bismark_mapping_report.txt" "$summary"
+else
+    cp "$tempdir/${outfile}_bismark_pe.sam" "$mapped"
+    cp "$tempdir/${outfile}_Bismark_paired-end_mapping_report.txt" "$summary"
+fi
+
+
+
+
+
+
+