<tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0+galaxy1">
  <description>based on quartile binning from FLOCK results</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
      python '$__tool_directory__/auto_collapse_pops.py' -o '${output}' -i '${input}' -p '${profile}' -r '${report}'
  ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/>
    <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/>
  </inputs>
  <outputs>
    <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/>
    <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowclr"/>
      <param name="profile" value="profile.flowscore"/>
      <param name="report" value="report.txt"/>
      <output name="output" file="output.flowclr" compare="sim_size"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool automatically collapses populations together based on FLOCK score profiles.

-----

.. class:: warningmark

*FLOCK score profiles are assigned based on quartile binning of the data. As always, use this tool with caution and be critical of your results*

-----

**Input**

FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each, as well as the file containing the score profiles for each FLOCK population.

**Output**

The input file with selected populations replaced by the indicated population. This tool also generates a report.

-----

**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      ... 3
   ...     ...     ...     ... ...

*Population profile file*::

   Population_ID Marker1 Marker2 Marker3 ... Count Percentage
   1             2       2       3       ... 3885  6.44
   2             1       3       4       ... 2774  4.62
   3             2       2       3       ... 2151  3.59
   4             1       3       2       ... 1207  2.01
   ...           ...     ...     ...     ... ...   ...

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

   Marker1 Marker2 Marker3 ... Population
   34      45      12      ... 1
   33      65      10      ... 4
   19      62      98      ... 2
   12      36      58      ... 1
   ...     ...     ...     ... ...

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

   New_Population Former_Populations Marker1 Marker2 Marker3 ...
   1              1, 3               2       2       3       ...
   2              2                  1       3       4       ...
   3              4                  1       3       2       ...
   4              5, 8, 12           3       1       1       ...
   ...            ...                ...     ...     ...     ...
  ]]>
  </help>
</tool>