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1 <tool id="gd_population_structure" name="Population" version="1.0.0">
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2 <description>structure</description>
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3
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4 <command interpreter="python">
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5 population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.extra_files_path" "$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="populations" type="integer" min="1" value="2" label="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="html" />
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15 </outputs>
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16
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17 <help>
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18 **What it does**
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19
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20 The users selects a set of data generated by the Galaxy tool to "prepare
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21 to look for population structure", and specifies a number, K, of ancestral
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22 populations. The tool estimates the proportion of each individual's ancestry
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23 coming from each ancestral population. The proportions are shown both as
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24 numbers and graphically.
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25
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26 **Acknowledgments**
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27
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28 We use the program "Admixture", downloaded from
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29
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30 http://www.genetics.ucla.edu/software/admixture/
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31
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32 and described in the paper "Fast model-based estimation of ancestry in
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33 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
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34 Genome Research 19 (2009), pp. 1655-1664.
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35 </help>
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36 </tool>
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