<tool id="generate_mfi" name="Generate the centroids" version="1.0">
  <description>from a flow result file</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
    <requirement type="package" version="1.10.2">numpy</requirement>
    <requirement type="package" version="0.16.0">scipy</requirement>
  </requirements>
  <stdio>
       <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/generateMFI.py -i "${input}" -o "${output}" -M "${mfi}"
  ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" label="Flow Text file"/>
    <param name="mfi" type="select" label="Calculate centroids using:">
      <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
      <option value="mdfi">Median Fluorescence Intensity</option>
      <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
    </param>
  </inputs>
  <outputs>
    <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="mfi"/>
      <output name="output" file="mfi.flowmfi"/>
    </test>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="mdfi"/>
      <output name="output" file="mdfi.flowmfi"/>
    </test>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="mfi" value="gmfi"/>
      <output name="output" file="gmfi.flowmfi"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of a FLOCK output file.

-----

**Input file**

This tool reads in a FLOCK output file.

**Output file**

The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK.

-----

**Example**

*Input*::

   Marker1 Marker2 Marker3 Population
   34      45      12      1
   13      65      10      5
   19      62      98      2
   32      46      10      1

*Output*::

   Population Marker1 Marker2 Marker3
   1          38      49      10
   2          21      63      100
   3          31      52      45
   4          11      78      25
  ]]>
  </help>
</tool>