comparison population_structure.xml @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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-1:000000000000 0:2c498d40ecde
1 <tool id="gd_population_structure" name="Population" version="1.0.0">
2 <description>structure</description>
3
4 <command interpreter="python">
5 population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.extra_files_path" "$populations"
6 </command>
7
8 <inputs>
9 <param name="input" type="data" format="wped" 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="wped" >
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 **What it does**
40
41 The users selects a set of data generated by the Galaxy tool to "prepare
42 to look for population structure", and specifies a number, K, of ancestral
43 populations. The tool estimates the proportion of each individual's ancestry
44 coming from each ancestral population. The proportions are shown both as
45 numbers and graphically.
46
47 **Acknowledgments**
48
49 We use the program "Admixture", downloaded from
50
51 http://www.genetics.ucla.edu/software/admixture/
52
53 and described in the paper "Fast model-based estimation of ancestry in
54 unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
55 Genome Research 19 (2009), pp. 1655-1664.
56 </help>
57 </tool>