[3] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | ## |
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| 4 | ## Galaxy wrapper for cut 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 | ## complement flag (might be empty string) |
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| 10 | ## what to cut (fields or characters) |
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| 11 | ## cut list (e.g. 1,2,3,4) |
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| 12 | ## input_file |
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| 13 | ## output_file |
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| 14 | |
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| 15 | COMPLEMENT="$1" |
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| 16 | CUTWHAT="$2" |
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| 17 | CUTLIST="$3" |
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| 18 | INPUT="$4" |
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| 19 | OUTPUT="$5" |
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| 20 | |
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| 21 | if [ -z "$OUTPUT" ]; then |
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| 22 | echo "This script should be run from inside galaxy!" >&2 |
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| 23 | exit 1 |
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| 24 | fi |
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| 25 | |
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| 26 | if [ ! -r "$INPUT" ]; then |
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| 27 | echo "error: input file ($INPUT) not found!" >&2 |
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| 28 | exit 1 |
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| 29 | fi |
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| 30 | |
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| 31 | # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset. |
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| 32 | # This way the user can tell what was the command |
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| 33 | if [ -z "$COMPLEMENT" ]; then |
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| 34 | echo -n "Extracting " |
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| 35 | else |
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| 36 | echo "Deleting " |
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| 37 | fi |
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| 38 | |
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| 39 | case $CUTWHAT in |
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| 40 | -f) echo -n "field(s) " |
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| 41 | ;; |
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| 42 | |
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| 43 | -c) echo -n "character(s) " |
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| 44 | ;; |
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| 45 | esac |
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| 46 | |
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| 47 | echo "$CUTLIST" |
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| 48 | |
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| 49 | |
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| 50 | cut $COMPLEMENT $CUTWHAT $CUTLIST < $INPUT > $OUTPUT |
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| 51 | |
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| 52 | exit |
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