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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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