galaxy/tools/filters/grep.xml

<tool id="Grep1" name="Select" version="1.0.4" profile="20.05">
  <description>lines that match an expression</description>
  <requirements>
    <requirement type="package" version="3.4">grep</requirement>
  </requirements>
  <edam_operations>
    <edam_operation>operation_3695</edam_operation>
  </edam_operations>
  <stdio>
    <exit_code range="2:" level="warning" description="Select failed" />
  </stdio>
  <command><![CDATA[
    set -eo pipefail;
    #if $keep_header
      head -n 1 '$input' > '$out_file1' &&
      tail -n +2 '$input'
    #else
      cat '$input'
    #end if
    | grep -P -f '$pattern_file' $invert >> '$out_file1'
  ]]></command>
  <configfiles>
    <configfile name="pattern_file">$pattern</configfile>
  </configfiles>
  <inputs>
    <param format="txt" name="input" type="data" label="Select lines from"/>
    <param name="invert" type="select" label="that">
      <option value="">Matching</option>
      <option value="-v">NOT Matching</option>
    </param>
    <param name="pattern" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
      <sanitizer>
        <valid initial="string.printable">
        </valid>
      </sanitizer>
    </param>
    <param name="keep_header" type="boolean" truevalue="true" falsevalue="false" label="Keep header line" help="i.e. the first line is kept independent of the regular expression"/>
  </inputs>
  <outputs>
    <data format_source="input" name="out_file1" metadata_source="input"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="1.bed"/>
      <param name="invert" value=""/>
      <param name="pattern" value="^chr[0-9]*"/>
      <output name="out_file1" file="fs-grep.dat"/>
    </test>
    <test>
      <param name="input" value="1.bed"/>
      <param name="invert" value=""/>
      <param name="pattern" value="+"/>
      <param name="keep_header" value="true"/>
      <output name="out_file1">
        <assert_contents>
          <has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
          <not_has_text text="CCDS993.1_cds_0_0_chr1_148078401_r"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="1.bed"/>
      <param name="invert" value=""/>
      <param name="pattern" value="+"/>
      <output name="out_file1">
        <assert_contents>
          <not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
          <not_has_text text="CCDS993.1_cds_0_0_chr1_148078401_r"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="1.bed"/>
      <param name="invert" value=""/>
      <param name="pattern" value="&lt;&gt;\&quot;[A]{1}"/>
      <param name="keep_header" value="true"/>
      <output name="out_file1">
        <assert_contents>
          <not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input" value="1.bed"/>
      <param name="invert" value=""/>
      <param name="pattern" value="147962192|147984545"/>
      <output name="out_file1">
        <assert_contents>
          <has_n_lines n="2"></has_n_lines>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>

.. class:: infomark

**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*

-----

**Syntax**

The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing 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.
- **\\A** 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.
- **\\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 is matched 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.

-----

**Example**

- **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file.
- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651.
- **(abc)|(def)** would match either "abc" or "def".
- **^\\W+#** would match any line that is a comment.
</help>
</tool>