Mercurial > repos > eugen > bs_seq_test_1
view bismark_wrapper.sh @ 0:10e211ab5e5c draft
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author | eugen |
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date | Mon, 13 Aug 2012 08:07:00 -0400 |
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#!/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