[3] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | # |
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| 4 | # NOTE: |
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| 5 | # This is a wrapper for GNU's join under galaxy |
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| 6 | # not ment to be used from command line (if you're using the command line, simply run 'join' directly...) |
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| 7 | # |
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| 8 | # All parameters must be supplied. |
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| 9 | # the join_tool.xml file takes care of that. |
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| 10 | |
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| 11 | JOINTYPE="$1" |
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| 12 | OUTPUT_FORMAT="$2" |
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| 13 | EMPTY_STRING="$3" |
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| 14 | DELIMITER="$4" |
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| 15 | IGNORE_CASE="$5" |
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| 16 | |
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| 17 | INPUT1="$6" |
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| 18 | COLUMN1="$7" |
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| 19 | INPUT2="$8" |
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| 20 | COLUMN2="$9" |
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| 21 | OUTPUT="${10}" |
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| 22 | |
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| 23 | if [ "$OUTPUT" == "" ]; then |
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| 24 | echo "This script is part of galaxy. Don't run it manually.\n" >&2 |
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| 25 | exit 1; |
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| 26 | fi |
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| 27 | |
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| 28 | #This a TAB hack for galaxy (which can't transfer a "\t" as a parameter) |
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| 29 | [ "$DELIMITER" == "tab" ] && DELIMITER=" " |
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| 30 | |
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| 31 | #Remove spaces from the output format (if the user entered any) |
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| 32 | OUTPUT_FORMAT=${OUTPUT_FORMAT// /} |
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| 33 | [ "$OUTPUT_FORMAT" != "" ] && OUTPUT_FORMAT="-o $OUTPUT_FORMAT" |
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| 34 | |
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| 35 | echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" |
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| 36 | #echo join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $IGNORE_CASE $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" \> "$OUTPUT" |
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| 37 | join $OUTPUT_FORMAT -t "$DELIMITER" -e "$EMPTY_STRING" $JOINTYPE -1 "$COLUMN1" -2 "$COLUMN2" "$INPUT1" "$INPUT2" > "$OUTPUT" || exit 1 |
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