| Previous changeset 2:41f30b042bac (2012-11-29) Next changeset 4:e5025e0378d0 (2012-11-29) |
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bsmap_wrapper.sh |
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| diff -r 41f30b042bac -r 91e88de226a3 bsmap_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsmap_wrapper.sh Thu Nov 29 10:10:16 2012 -0500 |
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| @@ -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 |