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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 ##
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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 ## regex
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12 ## COLOR or NOCOLOR
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13 ## [other parameters passed on to grep]
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14
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15 INPUT="$1"
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16 OUTPUT="$2"
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17 REGEX="$3"
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18 COLOR="$4"
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19
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20 shift 4
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21
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22 if [ -z "$COLOR" ]; then
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23 echo usage: $0 INPUTFILE OUTPUTFILE REGEX COLOR\|NOCOLOR [other grep patameters] >&2
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24 exit 1
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25 fi
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26
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27 if [ ! -r "$INPUT" ]; then
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28 echo "error: input file ($INPUT) not found!" >&2
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29 exit 1
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30 fi
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31
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32 # Messages printed to STDOUT will be displayed in the "INFO" field in the galaxy dataset.
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33 # This way the user can tell what was the command
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34 echo "grep" "$@" "$REGEX"
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35
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36 if [ "$COLOR" == "COLOR" ]; then
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37 #
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38 # What the heck is going on here???
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39 # 1. "GREP_COLORS" is an environment variable, telling GREP which ANSI colors to use.
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40 # 2. "--colors=always" tells grep to actually use colors (according to the GREP_COLORS variable)
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41 # 3. first sed command translates the ANSI color to a <FONT> tag with blue color (and a <B> tag, too)
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42 # 4. second sed command translates the no-color ANSI command to a </FONT> tag (and a </B> tag, too)
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43 # 5. htmlize_pre scripts takes a text input and wraps it in <HTML><BODY><PRE> tags, making it a fixed-font HTML file.
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44
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45 GREP_COLORS="ms=31" grep --color=always -P "$@" -- "$REGEX" "$INPUT" | \
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46 grep -v "^\[36m\[K--\[m\[K$" | \
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47 sed -r 's/\[[0123456789;]+m\[K?/<font color="blue"><b>/g' | \
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48 sed -r 's/\[m\[K?/<\/b><\/font>/g' | \
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49 htmlize_pre.sh > "$OUTPUT"
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50
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51
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52 if (( $? )); then exit; fi
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53
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54 elif [ "$COLOR" == "NOCOLOR" ]; then
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55 grep -P "$@" -- "$REGEX" "$INPUT" | grep -v "^--$" > "$OUTPUT"
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56 if (( $? )); then exit; fi
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57 else
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58 echo Error: third parameter must be "COLOR" or "NOCOLOR" >&2
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59 exit 1
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60 fi
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61
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62 exit 0
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