view grep.xml @ 0:ec66f9d90ef0 draft

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<tool id="unixtools_grep_tool" name="Search in textfiles" version="0.1.1">
    <description>(grep)</description>
    <requirements>
        <requirement type="package" version="8.21">gnu_coreutils</requirement>
        <requirement type="package" version="2.14">gnu_grep</requirement>
        <requirement type="set_environment">UNIX_TOOLS_SCRIPT_PATH</requirement>
    </requirements>
    <command interpreter="sh">
        #if $color = "COLOR":
            GREP_COLOR='1;34' grep --color=always -P "$@" -- "${url_paste}" '${input}' | \$UNIX_TOOLS_SCRIPT_PATH/ansi2html.sh > "${output}"
        #else:
            grep -P "$@" -- "${url_paste}" '${input}' | grep -v "^--$" > "${output}"
        #end if

        ##grep_wrapper.sh '$input' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
    </command>
    <inputs>
        <param format="txt" name="input" 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">
            <option value="-i">case insensitive</option>
            <option value="">case sensitive</option>
        </param>

        <param name="lines_before" type="integer"  label="Show lines preceding the matched line (-B)" help="leave it at zero unless you know what you're doing" value="0" />
        <param name="lines_after" type="integer"  label="Show lines trailing the matched line (-A)" help="leave it at zero unless you know what you're doing" value="0" />

        <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="input">
        <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="input" value="unix_grep_input1.txt" />
          <output name="output" file="unix_grep_output1.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" />
      </test>
      <test>
          <!-- grep a FASTA file for sequences with specific motif -
             show highlighed output -->
          <param name="input" value="unix_grep_input1.txt" />
          <output name="output" file="unix_grep_output2.html" />
          <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" />
      </test>
  </tests>
<help>

**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. 


</help>
</tool>