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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 <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="populations" value="2" />
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27
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28 <output name="output" file="genome_diversity/test_out/population_structure/population_structure.html" ftype="html" compare="diff" lines_diff="2">
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29 <extra_files type="file" name="numeric.txt" value="genome_diversity/test_out/population_structure/numeric.txt" />
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30 <extra_files type="file" name="graphical.pdf" value="genome_diversity/test_out/population_structure/graphical.pdf" compare="sim_size" delta="1000" />
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31 </output>
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32 </test>
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33 </tests>
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34
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35
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36 <help>
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37 **What it does**
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38
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39 The users selects a set of data generated by the Galaxy tool to "prepare
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40 to look for population structure", and specifies a number, K, of ancestral
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41 populations. The tool estimates the proportion of each individual's ancestry
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42 coming from each ancestral population. The proportions are shown both as
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43 numbers and graphically.
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44
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45 **Acknowledgments**
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46
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47 We use the program "Admixture", downloaded from
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48
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49 http://www.genetics.ucla.edu/software/admixture/
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50
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51 and described in the paper "Fast model-based estimation of ancestry in
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52 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
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53 Genome Research 19 (2009), pp. 1655-1664.
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54 </help>
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55 </tool>
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