<tool id="gd_assignment_of_optimal_breeding_pairs" name="Matings" version="1.0.0">
  <description>: Assignment of optimal breeding pairs</description>

  <command interpreter="python">
    assignment_of_optimal_breeding_pairs.py '$input' '$randomizations' '$output'
  </command>

  <inputs>
    <param name="input" type="data" format="txt" label="Pairs dataset" />
    <param name="randomizations" type="integer" min="0" value="0" label="Randomizations" />
  </inputs>

  <outputs>
    <data name="output" format="txt" />
  </outputs>

  <requirements>
    <requirement type="package" version="1.0.5.4">munkres</requirement>
  </requirements>

  <!--
  <tests>
  </tests>
  -->

  <help>

**Dataset formats**

The input and output datasets are in text_ format.

.. _text: ./static/formatHelp.html#text

The pairs dataset consists of lines of the form::

   name1  name2  prob

as generated by either of the &quot;Offspring estimated heterozygosity&quot; tools.

-----

**What it does**

The user supplies the offspring estimated heterozygosity for every
potential breeding pair, i.e., the expected fraction of autosomal SNPs
for which an offspring is heterozygous.  The tool assigns breeding
pairs to maximize the average estimated heterozygosity of the offspring.
Optionally, the user can specify a number of random assigned pairings,
for which the program reports the average estimated heterozygosity
of the offspring; this gives a comparison of the optimal and average
heterozygosity resulting from an assignment of breeding pairs.

  </help>
</tool>