--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/awk_wrapper.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,47 @@
+#!/bin/sh
+
+##
+## Galaxy wrapper for AWK command
+##
+
+##
+## command line arguments:
+##   input_file
+##   output_file
+##   awk-program
+##   input-field-separator
+##   output-field-separator
+
+INPUT="$1"
+OUTPUT="$2"
+PROG="$3"
+FS="$4"
+OFS="$5"
+
+shift 5
+
+if [ -z "$OFS" ]; then
+	echo usage: $0 INPUTFILE OUTPUTFILE AWK-PROGRAM FS OFS>&2
+	exit 1
+fi
+
+if [ ! -r "$INPUT" ]; then
+	echo "error: input file ($INPUT) not found!" >&2
+	exit 1
+fi
+
+if [ "$FS" == "tab" ]; then
+	FS="\t"
+fi
+if [ "$OFS" == "tab" ]; then
+	OFS="\t"
+fi
+
+# Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
+# This way the user can tell what was the command
+echo "awk" "$PROG"
+
+awk --sandbox -v OFS="$OFS" -v FS="$FS" --re-interval "$PROG" "$INPUT" > "$OUTPUT"
+if (( $? ));  then exit; fi
+
+exit 0