[3] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | ## |
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| 4 | ## Galaxy wrapper for AWK 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 | ## awk-program |
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| 12 | ## input-field-separator |
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| 13 | ## output-field-separator |
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| 14 | |
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| 15 | INPUT="$1" |
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| 16 | OUTPUT="$2" |
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| 17 | PROG="$3" |
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| 18 | FS="$4" |
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| 19 | OFS="$5" |
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| 20 | |
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| 21 | shift 5 |
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| 22 | |
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| 23 | if [ -z "$OFS" ]; then |
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| 24 | echo usage: $0 INPUTFILE OUTPUTFILE AWK-PROGRAM FS OFS>&2 |
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| 25 | exit 1 |
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| 26 | fi |
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| 27 | |
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| 28 | if [ ! -r "$INPUT" ]; then |
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| 29 | echo "error: input file ($INPUT) not found!" >&2 |
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| 30 | exit 1 |
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| 31 | fi |
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| 32 | |
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| 33 | if [ "$FS" == "tab" ]; then |
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| 34 | FS="\t" |
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| 35 | fi |
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| 36 | if [ "$OFS" == "tab" ]; then |
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| 37 | OFS="\t" |
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| 38 | fi |
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| 39 | |
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| 40 | # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset. |
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| 41 | # This way the user can tell what was the command |
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| 42 | echo "awk" "$PROG" |
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| 43 | |
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| 44 | awk --sandbox -v OFS="$OFS" -v FS="$FS" --re-interval "$PROG" "$INPUT" > "$OUTPUT" |
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| 45 | if (( $? )); then exit; fi |
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| 46 | |
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| 47 | exit 0 |
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