#!/bin/sh ## ## Galaxy wrapper for GREP command. ## ## ## 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 # # What the heck is going on here??? # 1. "GREP_COLORS" is an environment variable, telling GREP which ANSI colors to use. # 2. "--colors=always" tells grep to actually use colors (according to the GREP_COLORS variable) # 3. first sed command translates the ANSI color to a tag with blue color (and a tag, too) # 4. second sed command translates the no-color ANSI command to a tag (and a tag, too) # 5. htmlize_pre scripts takes a text input and wraps it in

 tags, making it a fixed-font HTML file.

	GREP_COLORS="ms=31" grep --color=always -P "$@" -- "$REGEX" "$INPUT" | \
		grep -v "^\[36m\[K--\[m\[K$" | \
		sed -r 's/\[[0123456789;]+m\[K?//g' | \
		sed -r 's/\[m\[K?/<\/b><\/font>/g' | \
		htmlize_pre.sh > "$OUTPUT"


	if (( $? ));  then exit; fi

elif [ "$COLOR" == "NOCOLOR" ]; then
	grep -P "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT"
	if (( $? ));  then exit; fi
else
	echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2
	exit 1
fi

exit 0