|
0
|
1 #!/usr/bin/env bash
|
|
|
2 #
|
|
|
3 # Galaxy wrapper for Aakrosh Ratan's ldtools
|
|
|
4 #
|
|
|
5
|
|
|
6 set -e
|
|
|
7
|
|
|
8 export PATH=$PATH:$(dirname $0)
|
|
|
9
|
|
|
10 ## pagetag options
|
|
|
11 input=
|
|
|
12 rsquare=0.64
|
|
|
13 freq=0.00
|
|
|
14 sample=###
|
|
|
15
|
|
|
16 ## senatag options
|
|
|
17 excluded=###
|
|
|
18 required=###
|
|
|
19 output=
|
|
|
20
|
|
|
21 until [ $# -eq 0 ]
|
|
|
22 do
|
|
|
23 case $1 in
|
|
|
24 rsquare=*)
|
|
|
25 rsquare=${1#rsquare=}
|
|
|
26 ;;
|
|
|
27 freq=*)
|
|
|
28 freq=${1#freq=}
|
|
|
29 ;;
|
|
|
30 input=*)
|
|
|
31 input=${1#input=}
|
|
|
32 ;;
|
|
|
33 output=*)
|
|
|
34 output=${1#output=}
|
|
|
35 ;;
|
|
|
36 *)
|
|
|
37 if [ -z "$new_args" ]; then
|
|
|
38 new_args=$1
|
|
|
39 else
|
|
|
40 new_args="$new_args $1"
|
|
|
41 fi
|
|
|
42 ;;
|
|
|
43 esac
|
|
|
44
|
|
|
45 shift
|
|
|
46 done
|
|
|
47
|
|
|
48 ## run pagetag
|
|
|
49 pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt &> /dev/null
|
|
|
50 if [ $? -ne 0 ]; then
|
|
|
51 echo "failed: pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt"
|
|
|
52 exit 1
|
|
|
53 fi
|
|
|
54
|
|
|
55 ## run sentag
|
|
|
56 senatag.py neighborhood.txt snps.txt > $output 2> /dev/null
|
|
|
57 if [ $? -ne 0 ]; then
|
|
|
58 echo "failed: senatag.py neighborhood.txt snps.txt"
|
|
|
59 exit 1
|
|
|
60 fi
|
|
|
61
|
|
|
62 ## cleanup
|
|
|
63 rm -f snps.txt neighborhood.txt
|
|
|
64
|
