view evaluate_population_numbers.xml @ 0:93ef08cd452b

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<tool id="gd_evaluate_population_numbers" name="Evaluate" version="1.0.0">
  <description>possible numbers of populations</description>

  <command interpreter="bash">
    evaluate_population_numbers.bash "${input.extra_files_path}/admix.ped" "$output" "$max_populations"
  </command>

  <inputs>
    <param name="input" type="data" format="wped" label="Dataset" />
    <param name="max_populations" type="integer" min="1" value="5" label="Maximum number of populations" />
  </inputs>

  <outputs>
    <data name="output" format="txt" />
  </outputs>

  <tests>
    <test>
      <param name='input' value='fake' ftype='wped' >
        <metadata name='base_name' value='admix' />
        <composite_data value='genome_diversity/test_out/prepare_population_structure/prepare_population_structure.html' />
        <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.ped' />
        <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.map' />
        <edit_attributes type='name' value='fake' />
      </param>
      <param name='max_populations' value='2' />

      <output name="output" file="genome_diversity/test_out/evaluate_population_numbers/evaluate_population_numbers.txt" />
    </test>
  </tests>

  <help>
**What it does**

The users selects a set of data generated by the Galaxy tool to "prepare
to look for population structure".  For all possible numbers K of ancestral
populations, from 1 up to a user-specified maximum, this tool produces values
that indicate how well the data can be explained as genotypes from individuals
derived from K ancestral populations.  These values are computed by a 5-fold
cross-validation procedure, so that a good choice for K will exhibit a low
cross-validation error compared with other potential settings for K.

**Acknowledgments**

We use the program "Admixture", downloaded from

http://www.genetics.ucla.edu/software/admixture/

and described in the paper "Fast model-based estimation of ancestry in
unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv"
flag to produce these values.
  </help>
</tool>