<tool id="extract_pop" name="Extract populations" version="1.0">
  <description>of interest from FLOCK or Cross Sample output.</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." />
    <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/extractpop.py -i "${input}" -o "${output}" -p "${population}" -m "${method}"
  ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" label="Source file"/>
    <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/>
  <param name="method" type="select" label="What would you like to do?">
    <option value="selected">Keep only these populations.</option>
    <option value="removed">Remove these populations.</option>
  </param>
  </inputs>
  <outputs>
    <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.txt"/>
      <param name="population" value="2,4"/>
    <param name="method" value="selected"/>
      <output name="output" file="output.flowtext"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool extracts events from given populations from FLOCK or Cross Sample outputs.

-----

**Input**

FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each.

**Output**

The input file filtered for selected populations.

-----

**Example 1**

*Input* - fluorescence intensities per marker and population ID per event::

   Marker1 Marker2 Marker3 Population
   34      45      12      1
   33      65      10      5
   19      62      98      2
   12      36      58      1

*Populations selected:* 2

*Method:* Keep only the selected populations

*Output* - fluorescence intensities per marker and population ID per event::

   Marker1 Marker2 Marker3 Population
   19      62      98      2

**Example 2**

*Input* - fluorescence intensities per marker and population ID per event::

   Marker1 Marker2 Marker3 Population
   34      45      12      1
   33      65      10      5
   19      62      98      2
   12      36      58      1

 *Populations selected:* 2

 *Method:* Remove the selected populations

 *Output* - fluorescence intensities per marker and population ID per event::

    Marker1 Marker2 Marker3 Population
    34      45      12      1
    33      65      10      5
    12      36      58      1

  ]]>
  </help>
</tool>