Mercurial > repos > miller-lab > genome_diversity
diff 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 |
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children | 5064f618ec1c |
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--- /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 @@ -0,0 +1,54 @@ +<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 "Offspring estimated heterozygosity" 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>