Mercurial > repos > eiriche > bsmap
comparison parsewig.sh @ 31:35cfb51eb545 draft
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author | eiriche |
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date | Mon, 03 Dec 2012 03:10:13 -0500 |
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30:c60a5a1ef9e8 | 31:35cfb51eb545 |
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1 #!/bin/bash | |
2 # | |
3 # Galaxy wrapper for WIG parser | |
4 # Written by Eugen Eirich @ Institute of Molecular Biology Mainz | |
5 # | |
6 | |
7 set -e | |
8 | |
9 | |
10 #get parameters | |
11 | |
12 until [ $# -eq 0 ] | |
13 do | |
14 case $1 in | |
15 input=*) | |
16 input=${1#input=} | |
17 ;; | |
18 extract=*) | |
19 extract=${1#extract=} | |
20 ;; | |
21 context=*) | |
22 context=${1#context=} | |
23 ;; | |
24 depth=*) | |
25 depth="cutoff=${1#depth=}" | |
26 ;; | |
27 cov_out=*) | |
28 cov_out=${1#cov_out=} | |
29 ;; | |
30 meth_out=*) | |
31 meth_out=${1#meth_out=} | |
32 ;; | |
33 esac | |
34 shift | |
35 done | |
36 | |
37 case $extract in | |
38 c) | |
39 output="-cov_out=$cov_out";; | |
40 m) | |
41 output="-meth_out=$meth_out";; | |
42 b) | |
43 output="-meth_out=$meth_out -cov_out=$cov_out";; | |
44 esac | |
45 | |
46 if [ "$context" != "" ] | |
47 then | |
48 context="-context=$context" | |
49 fi | |
50 | |
51 cd "$(dirname ${BASH_SOURCE[0]})" | |
52 perl wig_extractor.pl -e $extract $context $output $input 2>&1>/dev/null |