Mercurial > repos > eiriche > bsmap
changeset 30:c60a5a1ef9e8 draft
Deleted selected files
| author | eiriche |
|---|---|
| date | Mon, 03 Dec 2012 03:09:32 -0500 |
| parents | 0bc00f619bc7 |
| children | 35cfb51eb545 |
| files | parsewig.sh |
| diffstat | 1 files changed, 0 insertions(+), 51 deletions(-) [+] |
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--- a/parsewig.sh Mon Dec 03 02:53:01 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -#!/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