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<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.0">
    <description>(grep)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.14">gnu_grep</requirement>
        <requirement type="set_environment">TP_SCRIPT_PATH</requirement>
    </expand>
    <version_command>grep --version | head -n 1</version_command>
    <command>
<![CDATA[
        #if str($color) == "COLOR":
            GREP_COLOR='1;34'
            grep
                --color=always
                -P
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                -- "${url_paste}"
                '${infile}' | \$TP_SCRIPT_PATH/ansi2html.sh > "${output}"
        #else:
            grep
                -P
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                 -- "${url_paste}"
                '${infile}' | grep -v "^--$" > "${output}"
        #end if

        ##grep_wrapper.sh '$infile' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
]]>
    </command>
    <inputs>
        <param name="infile" format="txt" type="data" label="Select lines from" />

        <param name="invert" type="select" label="that">
            <option value="">Match</option>
            <option value="-v">Don't Match</option>
        </param>

        <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>

        <param name="case_sensitive" type="select" label="Match type" help="(-i)">
            <option value="-i">case insensitive</option>
            <option value="">case sensitive</option>
        </param>
        <param name="lines_before" type="integer" value="0"
            label="Show lines preceding the matched line" help="leave it at zero unless you know what you're doing. (-B)" />
        <param name="lines_after" type="integer" value="0"
            label="Show lines trailing the matched line" help="leave it at zero unless you know what you're doing. (-A)" />
        <param name="color" type="select"  label="Output">
            <option value="NOCOLOR">text file (for further processing)</option>
            <option value="COLOR">Highlighted HTML (for easier viewing)</option>
        </param>

    </inputs>
    <outputs>
        <data format="input" name="output" metadata_source="infile">
            <change_format>
                <when input="color" value="COLOR" format="html"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <!-- grep a FASTA file for sequences with specific motif -->
            <param name="infile" value="unix_grep_input1.txt" />
            <param name="case_sensitive" value="case sensitive" />
            <param name="invert" value="" />
            <param name="url_paste" value="AA.{2}GT" />
            <param name="lines_before" value="1" />
            <param name="lines_after" value="0" />
            <param name="color" value="NOCOLOR" />
            <output name="output" file="unix_grep_output1.txt" />
        </test>
        <test>
            <!-- grep a FASTA file for sequences with specific motif -
             show highlighed output -->
            <param name="infile" value="unix_grep_input1.txt" />
            <param name="case_sensitive" value="case sensitive" />
            <param name="invert" value="" />
            <param name="url_paste" value="AA.{2}GT" />
            <param name="lines_before" value="0" />
            <param name="lines_after" value="0" />
            <param name="color" value="COLOR" />
            <output name="output" file="unix_grep_output2.html" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool runs the unix **grep** command on the selected data file.

.. class:: infomark

**TIP:** This tool uses the **perl** regular expression syntax (same as running 'grep -P'). This is **NOT** the POSIX or POSIX-extended syntax (unlike the awk/sed tools).


**Further reading**

- Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
- Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
- Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)

-----

**Grep Examples**

- **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
- **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
- **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
- **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
 
-----

**Regular Expression Syntax**

The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. 

- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).
- **\\d** matches a digit, same as [0-9].
- **\\D** matches a non-digit.
- **\\s** matches a whitespace character.
- **\\S** matches anything BUT a whitespace.
- **\\t** matches a tab.
- **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
- **\\W** matches anything but an alphanumeric character.
- **(** .. **)** groups a particular pattern.
- **\\Z** matches the end of a string(but not a internal line).
- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.

  - **{n}** The preceding item is matched exactly n times.
  - **{n,}** The preceding item ismatched n or more times. 
  - **{n,m}** The preceding item is matched at least n times but not more than m times. 

- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
- **.** Matches any single character except a newline.
- ***** The preceding item will be matched zero or more times.
- **?** The preceding item is optional and matched at most once.
- **+** The preceding item will be matched one or more times.
- **^** has two meaning:
  - matches the beginning of a line or string. 
  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
- **$** matches the end of a line or string.
- **\|** Separates alternate possibilities. 

@REFERENCES@
]]>
    </help>
</tool>