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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 GREP command.
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5 ##
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6
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7 # The only truly portable way of getting a fully resolved path of a file.
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8 SCRIPT=$(perl -MCwd -e '$f=Cwd::realpath($ARGV[0]); die unless -e $f; print $f' "$0") || exit 1
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9 SCRIPT_DIR=$(dirname "$SCRIPT")
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10 ANSI_SCRIPT="$SCRIPT_DIR/ansi2html.sh"
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11 [ -e "$ANSI_SCRIPT" ] || { echo "Error: utility script ($ANSI_SCRIPT) not found." >&2 ; exit 1 ; }
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12
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13 ##
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14 ## command line arguments:
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15 ## input_file
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16 ## output_file
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17 ## regex
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18 ## COLOR or NOCOLOR
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19 ## [other parameters passed on to grep]
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20
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21 INPUT="$1"
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22 OUTPUT="$2"
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23 REGEX="$3"
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24 COLOR="$4"
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25
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26 shift 4
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27
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28 if [ -z "$COLOR" ]; then
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29 echo "usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR|NOCOLOR [other grep patameters]" >&2
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30 exit 1
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31 fi
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32
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33 if [ ! -r "$INPUT" ]; then
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34 echo "error: input file ($INPUT) not found!" >&2
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35 exit 1
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36 fi
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37
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38 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
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39 # This way the user can tell what was the command
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40 echo "grep" "$@" "$REGEX"
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41
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42 if [ "$COLOR" = "COLOR" ]; then
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43 GREP_COLOR='1;34' grep --color=always -P "$@" -- "$REGEX" "$INPUT" |
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44 sh "$ANSI_SCRIPT" > "$OUTPUT" || exit 1
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45
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46 elif [ "$COLOR" = "NOCOLOR" ]; then
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47 grep -P "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT" || exit 1
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48 else
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49 echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2
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50 exit 1
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51 fi
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