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annotate evaluate_population_numbers.xml @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
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1 <tool id="gd_evaluate_population_numbers" name="Population Complexity" version="1.0.0">
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2 <description>: Evaluate possible numbers of ancestral populations</description>
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3
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4 <command interpreter="bash">
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5 evaluate_population_numbers.bash "${input.extra_files_path}/admix.ped" "$output" "$max_populations"
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6 </command>
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7
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8 <inputs>
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9 <param name="input" type="data" format="gd_ped" label="Dataset" />
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10 <param name="max_populations" type="integer" min="1" value="5" label="Maximum number of populations" />
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11 </inputs>
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13 <outputs>
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14 <data name="output" format="txt" />
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15 </outputs>
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16
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17 <!--
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18 <tests>
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19 <test>
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20 <param name="input" value="fake" ftype="gd_ped" >
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21 <metadata name="base_name" value="admix" />
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22 <composite_data value="test_out/prepare_population_structure/prepare_population_structure.html" />
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23 <composite_data value="test_out/prepare_population_structure/admix.ped" />
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24 <composite_data value="test_out/prepare_population_structure/admix.map" />
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25 <edit_attributes type="name" value="fake" />
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26 </param>
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27 <param name="max_populations" value="2" />
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28
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29 <output name="output" file="test_out/evaluate_population_numbers/evaluate_population_numbers.txt" />
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30 </test>
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31 </tests>
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32 -->
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33
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34 <help>
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35
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36 **Dataset formats**
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37
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38 The input dataset is in gd_ped_ format.
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39 The output dataset is text. (`Dataset missing?`_)
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40
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41 .. _gd_ped: ./static/formatHelp.html#gd_ped
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42 .. _Dataset missing?: ./static/formatHelp.html
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43
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44 -----
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45
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46 **What it does**
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47
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48 The user selects a gd_ped dataset generated by the Prepare Input tool.
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49 For all possible numbers K of ancestral
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50 populations, from 1 up to a user-specified maximum, this tool produces values
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51 that indicate how well the data can be explained as genotypes from individuals
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52 derived from K ancestral populations. These values are computed by a 5-fold
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53 cross-validation procedure, so that a good choice for K will exhibit a low
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54 cross-validation error (CVE) compared with other potential settings for K.
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56 -----
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57
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58 **Acknowledgments**
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59
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60 We use the program "Admixture", downloaded from
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61
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62 http://www.genetics.ucla.edu/software/admixture/
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63
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64 and described in the paper "Fast model-based estimation of ancestry in
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65 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
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66 Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv"
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67 flag to produce these values.
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68
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69 -----
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70
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71 **Example**
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72
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73 - output with max populations of 6::
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74
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75 CVE (K=1): 1.10120
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76 CVE (K=2): 1.34683
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77 CVE (K=3): 1.80611
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78 CVE (K=4): 1.96339
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79 CVE (K=5): 1.21522
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80 CVE (K=6): 0.51501
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81
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82 </help>
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83 </tool>