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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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