<tool id="flowclr_stats" name="Generate summary statistics" version="1.0+galaxy0">
  <description>of FLOCK output</description>
  <requirements>
    <requirement type="package" version="0.17.1">pandas</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[
    python $__tool_directory__/flowclrstats.py -i '${input}' -p '${output}' -o '${report}'
 ]]>
  </command>
  <inputs>
    <param format="flowclr" name="input" type="data" collection_type="list" label="FLOCK file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Summary statistics of ${input.name}"/>
    <data format="tabular" name="report" label="Population report of ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.flowclr"/>
      <output name="output" file="out.tabular" />
      <output name="report" file="report.tabular" />
    </test>
  </tests>
  <help><![CDATA[
   This tool generates summary statistics on FLOCK output.

-----

**Input**

Any flowclr file, output from FLOCK or Cross Sample, containing fluorescence intensity value par marker and assigned population.

**Output**

This tool produces two reports. One indicates the population distribution in the input file, the other gives descriptive summary statistics per population and marker.

-----

**Example**

*Input* - fluorescence intensities per marker per event::

   Marker1 Marker2 Marker3 ... Population
   33      47      11      ... 1
   31      64      11      ... 6
   21      62      99      ... 2
   14      34      60      ... 7
   ...     ...     ...     ... ...


*Output* - Summary statistics::

   Population .    Marker1 Marker2 ...
   1          mean 188.7   71.7    ...
   1          std  49.6    40.2    ...
   1          min  107.0   0.0     ...
   1          25%  149.0   40.0    ...
   1          50%  183.0   77.0    ...
   1          75%  222.0   105.0   ...
   1          max  379.0   147.0   ...
   2          mean 36.8    186.5   ...
   2          std  40.6    50.5    ...
   2          min  0.0     119.0   ...
   2          25%  0.0     150.0   ...
   2          50%  20.0    174.0   ...
   2          75%  73.0    208.0   ...
   2          max  124.0   433.0   ...
   ...        ...  ...     ...     ...

*Output* - Population report::

   Population Count Percentage
   1          3866  43.92
   2          2772  31.50
   3          2163  24.58
   ...        ...   ...
   Total      8801
  ]]>
  </help>
</tool>