--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/unix_tools/cut_wrapper.sh	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,52 @@
+#!/bin/sh
+
+##
+## Galaxy wrapper for cut command.
+##
+
+##
+## command line arguments:
+##   complement flag (might be empty string)
+##   what to cut (fields or characters)
+##   cut list (e.g. 1,2,3,4)
+##   input_file
+##   output_file
+
+COMPLEMENT="$1"
+CUTWHAT="$2"
+CUTLIST="$3"
+INPUT="$4"
+OUTPUT="$5"
+
+if [ -z "$OUTPUT" ]; then
+	echo "This script should be run from inside galaxy!" >&2
+	exit 1
+fi
+
+if [ ! -r "$INPUT" ]; then
+	echo "error: input file ($INPUT) not found!" >&2
+	exit 1
+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
+if [ -z "$COMPLEMENT" ]; then
+	echo -n "Extracting " 
+else
+	echo "Deleting "
+fi
+
+case $CUTWHAT in
+	-f)	echo -n "field(s) "
+		;;
+		
+	-c)	echo -n "character(s) "
+		;;
+esac
+
+echo "$CUTLIST"
+
+
+cut $COMPLEMENT $CUTWHAT $CUTLIST < $INPUT > $OUTPUT
+
+exit