Mercurial > repos > eugen > bs_seq_test_2
annotate bsmap_meth_caller.sh @ 7:d49ae6a0ecda draft
Uploaded
| author | eugen |
|---|---|
| date | Thu, 16 Aug 2012 04:13:42 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| 7 | 1 #!/bin/bash |
| 2 # | |
| 3 # Galaxy wrapper for BSMAP Methylation Caller | |
| 4 # | |
| 5 | |
| 6 set -e | |
| 7 | |
| 8 #get parameters | |
| 9 | |
| 10 until [ $# -eq 0 ] | |
| 11 do | |
| 12 case $1 in | |
| 13 input=*) | |
| 14 input=${1#input=} | |
| 15 ;; | |
| 16 method=*) | |
| 17 method=${1#method=} | |
| 18 ;; | |
| 19 output=*) | |
| 20 output=${1#output=} | |
| 21 ;; | |
| 22 tempdir=*) | |
| 23 tempdir=${1#tempdir=} | |
| 24 ;; | |
| 25 ref=*) | |
| 26 ref=${1#ref=} | |
| 27 ;; | |
| 28 esac | |
| 29 shift | |
| 30 done | |
| 31 | |
| 32 #echo $ref | |
| 33 | |
| 34 python ~/dependencies/bsmap-2.6/methratio.py -o $output -d $ref -q $input |