<tool id="collapse_populations" name="Collapse populations" version="1.0+galaxy1">
  <description>from FLOCK or Cross Sample analysis</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="2" level="warning" description="The color code only allows populations between 1 and 40." />
    <exit_code range="3" level="warning" description="The same population to collapse into is being used several times." />
    <exit_code range="4" level="fatal" description="Please provide a comma separated list of populations to collapse." />
    <exit_code range="5" level="warning" description="The color code only allows populations between 1 and 40, and the same population to collapse into is being used several times." />
    <exit_code range="6" level="fatal" description="The populations must be integers (i.e,: 1,2,4.)" />
    <exit_code range="7" level="fatal" description="The same population is being collapsed into 2 different populations." />
  </stdio>
  <command><![CDATA[
      python '$__tool_directory__/collapse_pops.py' -o '${output}' -i '${input}' -p '${population}' -c '${collapse}'
    #for $repeats in $repeat_option
        -p '${repeats.population}'
        -c '${repeats.collapse}'
    #end for
  ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" label="Source file"/>
    <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
    <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
    <repeat name="repeat_option" title="more populations to manipulate:">
      <param name="population" type="text" label="Collapse the following populations:" value="i.e.:2,3,11,25"/>
      <param name="collapse" type="text" label="Into population:" value="i.e.:4"/>
    </repeat>
  </inputs>
  <outputs>
    <data format="flowclr" name="output" label="${input.name} with renamed populations"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="population" value="2,3,4"/>
      <param name="collapse" value="1"/>
      <output name="output" file="output.flowclr"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool collapses several populations into one.

-----

.. class:: warningmark

Tip: You can use this tool to assign specific colors to your populations in the FLOCK and Cross Sample overview tools. The color scheme we use is the following:

.. image:: ./static/images/flowtools/liz_colorcode.png

-----

**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 with selected populations replaced by the indicated population.

-----

**Example**

*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, 5

*Collapse into population:* 3

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

   Marker1 Marker2 Marker3 ... Population
   34      45      12      ... 1
   33      65      10      ... 3
   19      62      98      ... 3
   12      36      58      ... 1
   ...     ...     ...     ... ...

  ]]>
  </help>
</tool>