root/galaxy-central/tools/unix_tools/cut_tool.xml @ 3

<tool id="cshl_cut_tool" name="cut">
  <description>columns from files</description>
  <command interpreter="sh">
        cut_wrapper.sh '$complement' '$cutwhat' '$list' '$input' '$output'
  </command>

  <inputs>
        <param format="txt" name="input" type="data" label="file to cut" />
                
        <param name="complement" type="select" label="Operation">
              <option value="">Keep</option>
              <option value="--complement">Discard</option>
        </param>

        <param name="cutwhat" type="select" label="Cut by">
              <option value="-f">fields</option>
              <option value="-c">characters</option>
        </param>

        <param name="list" type="text" size="20" label="List of Fields/Characters/Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5" value = "" />
  </inputs>

  <tests>
          <test>
                  <param name="input" value="unix_cut_input1.txt" />
                  <output name="output" file="unix_cut_output1.txt" />
                  <param name="complement" value="Keep" />
                  <param name="cutwhat" value="fields" />
                  <param name="list"  value="1,3,4" />
          </test>
          <test>
                  <param name="input" value="unix_cut_input1.txt" />
                  <output name="output" file="unix_cut_output1.txt" />
                  <param name="complement" value="Discard" />
                  <param name="cutwhat" value="fields" />
                  <param name="list"  value="2" />
          </test>
  </tests>

  <outputs>
    <data format="input" name="output" metadata_source="input"/>
  </outputs>
  <help>

**What it does**

This tool runs the **cut** unix command, which extract or delete columns from a file.

-----

Field List Example:

**1,3,7** - Cut specific fields/characters.

**3-**    - Cut from the third field/character to the end of the line.

**2-5**   - Cut from the second to the fifth field/character.

**-8**    - Cut from the first to the eight field/characters.




Input Example::

    fruit       color   price   weight
    apple       red     1.4     0.5
    orange      orange  1.5     0.3
    banana      yellow  0.9     0.3


Output Example ( **Keeping fields 1,3,4** )::

    fruit       price   weight
    apple       1.4     0.5
    orange      1.5     0.3
    banana      0.9     0.3

Output Example ( **Discarding field 2** )::

    fruit       price   weight
    apple       1.4     0.5
    orange      1.5     0.3
    banana      0.9     0.3

Output Example ( **Keeping 3 characters** )::

    fru
    app
    ora
    ban

  </help>
</tool>