root/galaxy-central/tools/human_genome_variation/ldtools_wrapper.sh

#!/usr/bin/env bash
#
# Galaxy wrapper for Aakrosh Ratan's ldtools
# 

set -e

export PATH=$PATH:$(dirname $0)

## pagetag options
input=
rsquare=0.64
freq=0.00
sample=###

## senatag options
excluded=###
required=###
output=

until [ $# -eq 0 ]
do
  case $1 in
    rsquare=*)
      rsquare=${1#rsquare=}
      ;;
    freq=*)
      freq=${1#freq=}
      ;;
    input=*)
      input=${1#input=}
      ;;
    output=*)
      output=${1#output=}
      ;;
    *)
      if [ -z "$new_args" ]; then
        new_args=$1
      else
        new_args="$new_args $1"
      fi
      ;;
  esac

  shift
done

## run pagetag
pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt &> /dev/null
if [ $? -ne 0 ]; then
        echo "failed: pagetag.py --rsquare $rsquare --freq $freq $input snps.txt neighborhood.txt"
        exit 1
fi

## run sentag
senatag.py neighborhood.txt snps.txt > $output 2> /dev/null
if [ $? -ne 0 ]; then
        echo "failed: senatag.py neighborhood.txt snps.txt"
        exit 1
fi

## cleanup
rm -f snps.txt neighborhood.txt