/tools/human_genome_variation/ldtools_wrapper.sh

 1#!/usr/bin/env bash
 2#
 3# Galaxy wrapper for Aakrosh Ratan's ldtools
 4# 
 5
 6set -e
 7
 8export PATH=$PATH:$(dirname $0)
 9
10## pagetag options
11input=
12rsquare=0.64
13freq=0.00
14sample=###
15
16## senatag options
17excluded=###
18required=###
19output=
20
21until [ $# -eq 0 ]
22do
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
46done
47
48## run pagetag
49pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt &> /dev/null
50if [ $? -ne 0 ]; then
51	echo "failed: pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt"
52	exit 1
53fi
54
55## run sentag
56senatag.py neighborhood.txt snps.txt > $output 2> /dev/null
57if [ $? -ne 0 ]; then
58	echo "failed: senatag.py neighborhood.txt snps.txt"
59	exit 1
60fi
61
62## cleanup
63rm -f snps.txt neighborhood.txt
64