| Previous changeset 28:781b796c6b9c (2012-12-03) Next changeset 30:c60a5a1ef9e8 (2012-12-03) |
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Commit message:
Uploaded |
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added:
parsewig.sh |
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| diff -r 781b796c6b9c -r 0bc00f619bc7 parsewig.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/parsewig.sh Mon Dec 03 02:53:01 2012 -0500 |
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| @@ -0,0 +1,51 @@ +#!/bin/bash +# +# Galaxy wrapper for BSMAP Methylation Caller +# + +set -e + + +#get parameters + +until [ $# -eq 0 ] +do + case $1 in + input=*) + input=${1#input=} + ;; + extract=*) + extract=${1#extract=} + ;; + context=*) + context=${1#context=} + ;; + depth=*) + depth="cutoff=${1#depth=}" + ;; + cov_out=*) + cov_out=${1#cov_out=} + ;; + meth_out=*) + meth_out=${1#meth_out=} + ;; + esac + shift +done + +case $extract in + c) + output="-cov_out=$cov_out";; + m) + output="-meth_out=$meth_out";; + b) + output="-meth_out=$meth_out -cov_out=$cov_out";; +esac + +if [ "$context" != "" ] +then + context="-context=$context" +fi + + +perl ~/dependencies/wig-parser/wiggle_extractor.pl -e $extract $context $output $input 2>&1>/dev/null \ No newline at end of file |