diff assignment_of_optimal_breeding_pairs.xml @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assignment_of_optimal_breeding_pairs.xml	Fri Sep 20 13:25:27 2013 -0400
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+<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>