--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/join_tool.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+#
+# NOTE:
+#  This is a wrapper for GNU's join under galaxy
+#  not ment to be used from command line (if you're using the command line, simply run 'join' directly...)
+#
+# All parameters must be supplied.
+# the join_tool.xml file takes care of that.
+
+JOINTYPE="$1"
+OUTPUT_FORMAT="$2"
+EMPTY_STRING="$3"
+DELIMITER="$4"
+IGNORE_CASE="$5"
+
+INPUT1="$6"
+COLUMN1="$7"
+INPUT2="$8"
+COLUMN2="$9"
+OUTPUT="${10}"
+
+if [ "$OUTPUT" == "" ]; then	
+	echo "This script is part of galaxy. Don't run it manually.\n" >&2
+	exit 1;
+fi
+
+#This a TAB hack for galaxy (which can't transfer a "\t" as a parameter)
+[ "$DELIMITER" == "tab" ] && DELIMITER="	"
+
+#Remove spaces from the output format (if the user entered any)
+OUTPUT_FORMAT=${OUTPUT_FORMAT// /}
+[ "$OUTPUT_FORMAT" != "" ] && OUTPUT_FORMAT="-o $OUTPUT_FORMAT"
+
+echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" 
+#echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" \> "$OUTPUT" 
+join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" > "$OUTPUT" || exit 1