diff grep_wrapper.sh @ 0:631dfde45073 draft default tip

First tool-shed public version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/grep_wrapper.sh	Tue Oct 09 18:48:06 2012 -0400
@@ -0,0 +1,51 @@
+#!/bin/sh
+
+##
+## Galaxy wrapper for GREP command.
+##
+
+# The only truly portable way of getting a fully resolved path of a file.
+SCRIPT=$(perl -MCwd -e '$f=Cwd::realpath($ARGV[0]); die unless -e $f; print $f' "$0") || exit 1
+SCRIPT_DIR=$(dirname "$SCRIPT")
+ANSI_SCRIPT="$SCRIPT_DIR/ansi2html.sh"
+[ -e "$ANSI_SCRIPT" ] || { echo "Error: utility script ($ANSI_SCRIPT) not found." >&2 ; exit 1 ; }
+
+##
+## command line arguments:
+##   input_file
+##   output_file
+##   regex
+##   COLOR or NOCOLOR
+##   [other parameters passed on to grep]
+
+INPUT="$1"
+OUTPUT="$2"
+REGEX="$3"
+COLOR="$4"
+
+shift 4
+
+if [ -z "$COLOR" ]; then
+	echo "usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR|NOCOLOR [other grep patameters]" >&2
+	exit 1
+fi
+
+if [ ! -r "$INPUT" ]; then
+	echo "error: input file ($INPUT) not found!" >&2
+	exit 1
+fi
+
+# Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
+# This way the user can tell what was the command
+echo "grep" "$@" "$REGEX"
+
+if [ "$COLOR" = "COLOR" ]; then
+	GREP_COLOR='1;34' grep --color=always -P "$@" -- "$REGEX" "$INPUT" |
+		sh "$ANSI_SCRIPT" > "$OUTPUT" || exit 1
+
+elif [ "$COLOR" = "NOCOLOR" ]; then
+	grep -P "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT" || exit 1
+else
+	echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2
+	exit 1
+fi