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annotate assignment_of_optimal_breeding_pairs.xml @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
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1 <tool id="gd_assignment_of_optimal_breeding_pairs" name="Matings" version="1.0.0">
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2 <description>: Assignment of optimal breeding pairs</description>
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3
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4 <command interpreter="python">
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5 assignment_of_optimal_breeding_pairs.py '$input' '$randomizations' '$output'
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6 </command>
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7
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8 <inputs>
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9 <param name="input" type="data" format="txt" label="Pairs dataset" />
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10 <param name="randomizations" type="integer" min="0" value="0" label="Randomizations" />
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11 </inputs>
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12
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13 <outputs>
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14 <data name="output" format="txt" />
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15 </outputs>
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17 <!--
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18 <requirements>
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19 <requirement type="package" version="1.0.5.4">munkres</requirement>
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20 </requirements>
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21 -->
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23 <!--
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24 <tests>
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25 </tests>
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26 -->
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27
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28 <help>
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29
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30 **Dataset formats**
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32 The input and output datasets are in text_ format.
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34 .. _text: ./static/formatHelp.html#text
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35
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36 The pairs dataset consists of lines of the form::
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38 name1 name2 prob
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40 as generated by either of the &quot;Offspring estimated heterozygosity&quot; tools.
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41
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42 -----
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43
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44 **What it does**
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46 The user supplies the offspring estimated heterozygosity for every
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47 potential breeding pair, i.e., the expected fraction of autosomal SNPs
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48 for which an offspring is heterozygous. The tool assigns breeding
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49 pairs to maximize the average estimated heterozygosity of the offspring.
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50 Optionally, the user can specify a number of random assigned pairings,
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51 for which the program reports the average estimated heterozygosity
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52 of the offspring; this gives a comparison of the optimal and average
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53 heterozygosity resulting from an assignment of breeding pairs.
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54
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55 </help>
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56 </tool>