Mercurial > repos > miller-lab > genome_diversity
annotate population_structure.xml @ 9:22fe0154fa54
added support for heterochromatic regions
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 10 Jul 2012 11:41:22 -0400 |
| parents | 7a94f11fe71f |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_population_structure" name="Population" version="1.0.0"> |
| 2 <description>structure</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
|
4
7a94f11fe71f
change output.extra_files_path to output.files_path
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
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5 population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.files_path" "$populations" |
| 0 | 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> |