Mercurial > repos > eugen > bs_seq_test_1
changeset 13:ee3bd6ad3958 draft
Uploaded
author | eugen |
---|---|
date | Wed, 15 Aug 2012 08:53:06 -0400 |
parents | 1d29aebf96ae |
children | 120a27b53be7 |
files | bismark_wrapper.sh |
diffstat | 1 files changed, 112 insertions(+), 0 deletions(-) [+] |
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--- /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 + + + + + + +