[3] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | ## |
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| 4 | ## Galaxy wrapper for SED 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 | ## sed-program |
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| 12 | ## [other parameters passed on to sed] |
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| 13 | |
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| 14 | INPUT="$1" |
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| 15 | OUTPUT="$2" |
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| 16 | PROG="$3" |
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| 17 | |
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| 18 | shift 3 |
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| 19 | |
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| 20 | if [ -z "$PROG" ]; then |
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| 21 | echo usage: $0 INPUTFILE OUTPUTFILE SED-PROGRAM [other sed patameters] >&2 |
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| 22 | exit 1 |
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| 23 | fi |
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| 24 | |
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| 25 | if [ ! -r "$INPUT" ]; then |
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| 26 | echo "error: input file ($INPUT) not found!" >&2 |
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| 27 | exit 1 |
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| 28 | fi |
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| 29 | |
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| 30 | # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset. |
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| 31 | # This way the user can tell what was the command |
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| 32 | echo "sed" "$@" "$PROG" |
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| 33 | |
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| 34 | sed -r --sandbox "$@" "$PROG" "$INPUT" > "$OUTPUT" |
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| 35 | if (( $? )); then exit; fi |
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| 36 | |
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| 37 | exit 0 |
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