Mercurial > repos > eugen > bs_seq_test_1
changeset 11:7ad77d2e23d0 draft
Uploaded
author | eugen |
---|---|
date | Wed, 15 Aug 2012 08:27:03 -0400 |
parents | 35df90c1f4aa |
children | 1d29aebf96ae |
files | bismark_meth_caller.sh |
diffstat | 1 files changed, 35 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark_meth_caller.sh Wed Aug 15 08:27:03 2012 -0400 @@ -0,0 +1,35 @@ +#!/bin/bash +# +# Galaxy wrapper for Bismark Methylation Caller +# + +set -e + +#get parameters + +until [ $# -eq 0 ] +do + case $1 in + input=*) + input=${1#input=} + ;; + method=*) + method=${1#method=} + ;; + output=*) + output=${1#output=} + ;; + tempdir=*) + tempdir=${1#tempdir=} + ;; + esac + shift +done +(grep ^@ $input; grep -v ^@ $input | sort -k3,3 -k1,1) > $tempdir"bismark_sam_sorted.sam" +methylation_extractor -$method -o $output $tempdir"bismark_sam_sorted.sam" 2>&1 > /dev/null + + + + + +