Mercurial > repos > miller-lab > genome_diversity
comparison assignment_of_optimal_breeding_pairs.xml @ 31:a631c2f6d913
Update to Miller Lab devshed revision 3c4110ffacc3
| author | Richard Burhans <burhans@bx.psu.edu> |
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| date | Fri, 20 Sep 2013 13:25:27 -0400 |
| parents | |
| children | 5064f618ec1c |
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| 30:4188853b940b | 31:a631c2f6d913 |
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| 1 <tool id="gd_assignment_of_optimal_breeding_pairs" name="Matings" version="1.0.0"> | |
| 2 <description>: Assignment of optimal breeding pairs</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 assignment_of_optimal_breeding_pairs.py '$input' '$randomizations' '$output' | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="txt" label="Pairs dataset" /> | |
| 10 <param name="randomizations" type="integer" min="0" value="0" label="Randomizations" /> | |
| 11 </inputs> | |
| 12 | |
| 13 <outputs> | |
| 14 <data name="output" format="txt" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <requirements> | |
| 18 <requirement type="package" version="1.0.5.4">munkres</requirement> | |
| 19 </requirements> | |
| 20 | |
| 21 <!-- | |
| 22 <tests> | |
| 23 </tests> | |
| 24 --> | |
| 25 | |
| 26 <help> | |
| 27 | |
| 28 **Dataset formats** | |
| 29 | |
| 30 The input and output datasets are in text_ format. | |
| 31 | |
| 32 .. _text: ./static/formatHelp.html#text | |
| 33 | |
| 34 The pairs dataset consists of lines of the form:: | |
| 35 | |
| 36 name1 name2 prob | |
| 37 | |
| 38 as generated by either of the "Offspring estimated heterozygosity" tools. | |
| 39 | |
| 40 ----- | |
| 41 | |
| 42 **What it does** | |
| 43 | |
| 44 The user supplies the offspring estimated heterozygosity for every | |
| 45 potential breeding pair, i.e., the expected fraction of autosomal SNPs | |
| 46 for which an offspring is heterozygous. The tool assigns breeding | |
| 47 pairs to maximize the average estimated heterozygosity of the offspring. | |
| 48 Optionally, the user can specify a number of random assigned pairings, | |
| 49 for which the program reports the average estimated heterozygosity | |
| 50 of the offspring; this gives a comparison of the optimal and average | |
| 51 heterozygosity resulting from an assignment of breeding pairs. | |
| 52 | |
| 53 </help> | |
| 54 </tool> |