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annotate population_structure.xml @ 18:f04f40a36cc8

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Latest changes from Belinda and Cathy. Webb's updates to the Fst tools.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 23 Oct 2012 12:41:52 -0400
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1 <tool id="gd_population_structure" name="Ancestry" version="1.0.0">
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2 <description>: Characterize ancestries w.r.t. inferred ancestral populations</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.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="gd_ped" 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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13 <outputs>
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14 <data name="output" format="html" />
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15 </outputs>
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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="populations" value="2" />
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29 <output name="output" file="test_out/population_structure/population_structure.html" ftype="html" compare="diff" lines_diff="2">
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30 <extra_files type="file" name="numeric.txt" value="test_out/population_structure/numeric.txt" />
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31 <extra_files type="file" name="graphical.pdf" value="test_out/population_structure/graphical.pdf" compare="sim_size" delta="1000" />
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32 </output>
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33 </test>
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34 </tests>
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35 -->
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37
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38 <help>
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39
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40 **Dataset formats**
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41
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42 The input dataset is in gd_ped_ format.
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43 The output dataset is a composite dataset containing a graph and text.
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44 (`Dataset missing?`_)
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45
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46 .. _gd_ped: ./static/formatHelp.html#gd_ped
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47 .. _Dataset missing?: ./static/formatHelp.html
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49 -----
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50
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51 **What it does**
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52
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53 The user selects a gd_ped dataset generated by the Prepare Input tool,
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54 and specifies a number, K, of ancestral
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55 populations. The tool estimates the proportion of each individual's ancestry
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56 coming from each ancestral population. The proportions are shown both as
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57 numbers and graphically.
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59 -----
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60
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61 **Acknowledgments**
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62
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63 We use the program "Admixture", downloaded from
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64
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65 http://www.genetics.ucla.edu/software/admixture/
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66
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67 and described in the paper "Fast model-based estimation of ancestry in
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68 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
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69 Genome Research 19 (2009), pp. 1655-1664.
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70
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71 </help>
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72 </tool>