--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/BEAM2_wrapper.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,75 @@
+#!/usr/bin/env bash
+#
+# Galaxy wrapper for Yu Zhang's BEAM2 adds two new options
+#  significance=foo    renames significance.txt to foo after BEAM2 is run
+#  posterior=bar       renames posterior.txt    to bar after BEAM2 is run
+# 
+
+set -e
+
+export PATH=$PATH:$(dirname $0)
+
+## options
+significance=
+posterior=
+new_args=
+map=
+ped=
+
+TFILE="/tmp/BEAM2.$$.tmp"
+
+## separate significance and posterior arguments from arguments to BEAM2
+until [ $# -eq 0 ]
+do
+  case $1 in
+    significance=*)
+      significance=${1#significance=}
+      ;;
+    posterior=*)
+      posterior=${1#posterior=}
+      ;;
+    map=*)
+      map=${1#map=}
+      ;;
+    ped=*)
+      ped=${1#ped=}
+      ;;
+    *)
+      if [ -z "$new_args" ]; then
+        new_args=$1
+      else
+        new_args="$new_args $1"
+      fi
+      ;;
+  esac
+
+  shift
+done
+
+## convert input for use with BEAM2
+lped_to_geno.pl $map $ped > $TFILE
+if [ $? -ne 0 ]; then
+  echo "failed: lped_to_geno.pl $map $ped > $TFILE"
+  exit 1
+fi
+
+## run BEAM2
+BEAM2 $TFILE $new_args 1>/dev/null
+if [ $? -ne 0 ]; then
+  echo "failed: BEAM2 $TFILE $new_args"
+  exit 1
+fi
+
+mergeSnps.pl significance.txt $TFILE
+if [ $? -ne 0 ]; then
+  echo "failed: mergeSnps.pl significance.txt $TFILE"
+  exit 1
+fi
+
+## move output files
+mv significance.txt $significance
+mv posterior.txt $posterior
+
+## cleanup
+rm -f $TFILE
+