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1 <tool id="gd_evaluate_population_numbers" name="Evaluate" version="1.0.0">
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2 <description>possible numbers of 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="wped" 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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12
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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 <tests>
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18 <test>
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19 <param name='input' value='fake' ftype='wped' >
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20 <metadata name='base_name' value='admix' />
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21 <composite_data value='genome_diversity/test_out/prepare_population_structure/prepare_population_structure.html' />
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22 <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.ped' />
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23 <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.map' />
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24 <edit_attributes type='name' value='fake' />
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25 </param>
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26 <param name='max_populations' value='2' />
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27
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28 <output name="output" file="genome_diversity/test_out/evaluate_population_numbers/evaluate_population_numbers.txt" />
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29 </test>
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30 </tests>
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31
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32 <help>
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33 **What it does**
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34
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35 The users selects a set of data generated by the Galaxy tool to "prepare
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36 to look for population structure". For all possible numbers K of ancestral
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37 populations, from 1 up to a user-specified maximum, this tool produces values
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38 that indicate how well the data can be explained as genotypes from individuals
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39 derived from K ancestral populations. These values are computed by a 5-fold
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40 cross-validation procedure, so that a good choice for K will exhibit a low
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41 cross-validation error compared with other potential settings for K.
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42
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43 **Acknowledgments**
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44
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45 We use the program "Admixture", downloaded from
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46
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47 http://www.genetics.ucla.edu/software/admixture/
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48
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49 and described in the paper "Fast model-based estimation of ancestry in
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50 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
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51 Genome Research 19 (2009), pp. 1655-1664. Admixture is called with the "--cv"
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52 flag to produce these values.
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53 </help>
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54 </tool>
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