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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 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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