|
12
|
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.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 **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>
|
