comparison population_structure.xml @ 14:8ae67e9fb6ff

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author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
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13:fdb4240fb565 14:8ae67e9fb6ff
1 <tool id="gd_population_structure" name="Ancestry" version="1.0.0">
2 <description>: Characterize ancestries w.r.t. inferred ancestral populations</description>
3
4 <command interpreter="python">
5 population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.files_path" "$populations"
6 </command>
7
8 <inputs>
9 <param name="input" type="data" format="gd_ped" label="Dataset" />
10 <param name="populations" type="integer" min="1" value="2" label="Number of populations" />
11 </inputs>
12
13 <outputs>
14 <data name="output" format="html" />
15 </outputs>
16
17 <!--
18 <tests>
19 <test>
20 <param name="input" value="fake" ftype="gd_ped" >
21 <metadata name="base_name" value="admix" />
22 <composite_data value="test_out/prepare_population_structure/prepare_population_structure.html" />
23 <composite_data value="test_out/prepare_population_structure/admix.ped" />
24 <composite_data value="test_out/prepare_population_structure/admix.map" />
25 <edit_attributes type="name" value="fake" />
26 </param>
27 <param name="populations" value="2" />
28
29 <output name="output" file="test_out/population_structure/population_structure.html" ftype="html" compare="diff" lines_diff="2">
30 <extra_files type="file" name="numeric.txt" value="test_out/population_structure/numeric.txt" />
31 <extra_files type="file" name="graphical.pdf" value="test_out/population_structure/graphical.pdf" compare="sim_size" delta="1000" />
32 </output>
33 </test>
34 </tests>
35 -->
36
37
38 <help>
39
40 **Dataset formats**
41
42 The input dataset is in gd_ped_ format.
43 The output dataset is a composite dataset containing a graph and text.
44 (`Dataset missing?`_)
45
46 .. _gd_ped: ./static/formatHelp.html#gd_ped
47 .. _Dataset missing?: ./static/formatHelp.html
48
49 -----
50
51 **What it does**
52
53 The user selects a gd_ped dataset generated by the Prepare Input tool,
54 and specifies a number, K, of ancestral
55 populations. The tool estimates the proportion of each individual's ancestry
56 coming from each ancestral population. The proportions are shown both as
57 numbers and graphically.
58
59 -----
60
61 **Acknowledgments**
62
63 We use the program "Admixture", downloaded from
64
65 http://www.genetics.ucla.edu/software/admixture/
66
67 and described in the paper "Fast model-based estimation of ancestry in
68 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
69 Genome Research 19 (2009), pp. 1655-1664.
70
71 </help>
72 </tool>