[3] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | ## |
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| 4 | ## Galaxy wrapper for GREP command. |
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| 5 | ## |
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| 6 | |
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| 7 | ## |
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| 8 | ## command line arguments: |
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| 9 | ## input_file |
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| 10 | ## output_file |
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| 11 | ## regex |
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| 12 | ## COLOR or NOCOLOR |
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| 13 | ## [other parameters passed on to grep] |
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| 14 | |
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| 15 | INPUT="$1" |
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| 16 | OUTPUT="$2" |
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| 17 | REGEX="$3" |
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| 18 | COLOR="$4" |
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| 19 | |
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| 20 | shift 4 |
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| 21 | |
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| 22 | if [ -z "$COLOR" ]; then |
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| 23 | echo usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR\|NOCOLOR [other grep patameters] >&2 |
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| 24 | exit 1 |
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| 25 | fi |
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| 26 | |
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| 27 | if [ ! -r "$INPUT" ]; then |
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| 28 | echo "error: input file ($INPUT) not found!" >&2 |
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| 29 | exit 1 |
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| 30 | fi |
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| 31 | |
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| 32 | # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset. |
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| 33 | # This way the user can tell what was the command |
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| 34 | echo "grep" "$@" "$REGEX" |
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| 35 | |
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| 36 | if [ "$COLOR" == "COLOR" ]; then |
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| 37 | # |
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| 38 | # What the heck is going on here??? |
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| 39 | # 1. "GREP_COLORS" is an environment variable, telling GREP which ANSI colors to use. |
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| 40 | # 2. "--colors=always" tells grep to actually use colors (according to the GREP_COLORS variable) |
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| 41 | # 3. first sed command translates the ANSI color to a <FONT> tag with blue color (and a <B> tag, too) |
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| 42 | # 4. second sed command translates the no-color ANSI command to a </FONT> tag (and a </B> tag, too) |
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| 43 | # 5. htmlize_pre scripts takes a text input and wraps it in <HTML><BODY><PRE> tags, making it a fixed-font HTML file. |
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| 44 | |
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| 45 | GREP_COLORS="ms=31" grep --color=always -P "$@" -- "$REGEX" "$INPUT" | \ |
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| 46 | grep -v "^\[36m\[K--\[m\[K$" | \ |
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| 47 | sed -r 's/\[[0123456789;]+m\[K?/<font color="blue"><b>/g' | \ |
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| 48 | sed -r 's/\[m\[K?/<\/b><\/font>/g' | \ |
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| 49 | htmlize_pre.sh > "$OUTPUT" |
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| 50 | |
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| 51 | |
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| 52 | if (( $? )); then exit; fi |
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| 53 | |
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| 54 | elif [ "$COLOR" == "NOCOLOR" ]; then |
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| 55 | grep -P "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT" |
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| 56 | if (( $? )); then exit; fi |
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| 57 | else |
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| 58 | echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2 |
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| 59 | exit 1 |
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| 60 | fi |
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| 61 | |
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| 62 | exit 0 |
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