Mercurial > repos > greg > bad_tool_config
comparison evaluate_population_numbers.xml @ 0:93ef08cd452b
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| author | greg |
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| date | Mon, 16 Apr 2012 14:20:32 -0400 |
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| -1:000000000000 | 0:93ef08cd452b |
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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="wped" 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 <tests> | |
| 18 <test> | |
| 19 <param name='input' value='fake' ftype='wped' > | |
| 20 <metadata name='base_name' value='admix' /> | |
| 21 <composite_data value='genome_diversity/test_out/prepare_population_structure/prepare_population_structure.html' /> | |
| 22 <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.ped' /> | |
| 23 <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.map' /> | |
| 24 <edit_attributes type='name' value='fake' /> | |
| 25 </param> | |
| 26 <param name='max_populations' value='2' /> | |
| 27 | |
| 28 <output name="output" file="genome_diversity/test_out/evaluate_population_numbers/evaluate_population_numbers.txt" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 | |
| 32 <help> | |
| 33 **What it does** | |
| 34 | |
| 35 The users selects a set of data generated by the Galaxy tool to "prepare | |
| 36 to look for population structure". For all possible numbers K of ancestral | |
| 37 populations, from 1 up to a user-specified maximum, this tool produces values | |
| 38 that indicate how well the data can be explained as genotypes from individuals | |
| 39 derived from K ancestral populations. These values are computed by a 5-fold | |
| 40 cross-validation procedure, so that a good choice for K will exhibit a low | |
| 41 cross-validation error compared with other potential settings for K. | |
| 42 | |
| 43 **Acknowledgments** | |
| 44 | |
| 45 We use the program "Admixture", downloaded from | |
| 46 | |
| 47 http://www.genetics.ucla.edu/software/admixture/ | |
| 48 | |
| 49 and described in the paper "Fast model-based estimation of ancestry in | |
| 50 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange, | |
| 51 Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv" | |
| 52 flag to produce these values. | |
| 53 </help> | |
| 54 </tool> |