--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/ldtools_wrapper.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,64 @@
+#!/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
+