Mercurial > repos > miller-lab > genome_diversity
comparison evaluate_population_numbers.xml @ 12:4b6590dd7250
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| author | miller-lab |
|---|---|
| date | Wed, 12 Sep 2012 17:10:26 -0400 |
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| 11:d4ec09e8079f | 12:4b6590dd7250 |
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| 1 <tool id="gd_evaluate_population_numbers" name="Evaluate" version="1.0.0"> | |
| 2 <description>possible numbers of populations</description> | |
| 3 | |
| 4 <command interpreter="bash"> | |
| 5 evaluate_population_numbers.bash "${input.extra_files_path}/admix.ped" "$output" "$max_populations" | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param name="input" type="data" format="gd_ped" label="Dataset" /> | |
| 10 <param name="max_populations" type="integer" min="1" value="5" label="Maximum number of populations" /> | |
| 11 </inputs> | |
| 12 | |
| 13 <outputs> | |
| 14 <data name="output" format="txt" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <!-- | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="input" value="fake" ftype="gd_ped" > | |
| 21 <metadata name="base_name" value="admix" /> | |
| 22 <composite_data value="test_out/prepare_population_structure/prepare_population_structure.html" /> | |
| 23 <composite_data value="test_out/prepare_population_structure/admix.ped" /> | |
| 24 <composite_data value="test_out/prepare_population_structure/admix.map" /> | |
| 25 <edit_attributes type="name" value="fake" /> | |
| 26 </param> | |
| 27 <param name="max_populations" value="2" /> | |
| 28 | |
| 29 <output name="output" file="test_out/evaluate_population_numbers/evaluate_population_numbers.txt" /> | |
| 30 </test> | |
| 31 </tests> | |
| 32 --> | |
| 33 | |
| 34 <help> | |
| 35 **What it does** | |
| 36 | |
| 37 The users selects a set of data generated by the Galaxy tool to "prepare | |
| 38 to look for population structure". For all possible numbers K of ancestral | |
| 39 populations, from 1 up to a user-specified maximum, this tool produces values | |
| 40 that indicate how well the data can be explained as genotypes from individuals | |
| 41 derived from K ancestral populations. These values are computed by a 5-fold | |
| 42 cross-validation procedure, so that a good choice for K will exhibit a low | |
| 43 cross-validation error compared with other potential settings for K. | |
| 44 | |
| 45 **Acknowledgments** | |
| 46 | |
| 47 We use the program "Admixture", downloaded from | |
| 48 | |
| 49 http://www.genetics.ucla.edu/software/admixture/ | |
| 50 | |
| 51 and described in the paper "Fast model-based estimation of ancestry in | |
| 52 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange, | |
| 53 Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv" | |
| 54 flag to produce these values. | |
| 55 </help> | |
| 56 </tool> |