# HG changeset patch
# User eugen
# Date 1345035160 14400
# Node ID 1d29aebf96aea4ca90b38ec127471bd43ce7e5e9
# Parent  7ad77d2e23d03f33fed13097a4e6078b21c2a06a
Deleted selected files

diff -r 7ad77d2e23d0 -r 1d29aebf96ae bismark_meth_caller.sh
--- a/bismark_meth_caller.sh	Wed Aug 15 08:27:03 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/bin/bash
-#
-# Galaxy wrapper for Bismark 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=}
-			;;
-	esac
-	shift
-done
-(grep ^@ $input; grep -v ^@ $input | sort -k3,3 -k1,1) > $tempdir"bismark_sam_sorted.sam"
-methylation_extractor -$method -o $output $tempdir"bismark_sam_sorted.sam" 2>&1 > /dev/null
-
-
-
-
-
-
diff -r 7ad77d2e23d0 -r 1d29aebf96ae bismark_wrapper.sh
--- a/bismark_wrapper.sh	Wed Aug 15 08:27:03 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-#!/bin/bash
-#
-# Galaxy wrapper for Bismark
-#
-
-set -e
-
-export PATH="/home/galaxy/dependencies/bismark:$PATH"
-export PATH="/home/galaxy/dependencies/diverse:$PATH"
-
-#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
-
-
-
-
-
-
-