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
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>