Mercurial > repos > eugen > bs_seq_test_2
changeset 7:d49ae6a0ecda draft
Uploaded
| author | eugen |
|---|---|
| date | Thu, 16 Aug 2012 04:13:42 -0400 |
| parents | 54492fec12ba |
| children | 87af1f51d270 |
| files | bsmap_meth_caller.sh |
| diffstat | 1 files changed, 34 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsmap_meth_caller.sh Thu Aug 16 04:13:42 2012 -0400 @@ -0,0 +1,34 @@ +#!/bin/bash +# +# Galaxy wrapper for BSMAP 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=${1#tempdir=} + ;; + ref=*) + ref=${1#ref=} + ;; + esac + shift +done + +#echo $ref + +python ~/dependencies/bsmap-2.6/methratio.py -o $output -d $ref -q $input \ No newline at end of file