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comparison admixture.xml @ 4:58df6910f1c3 draft

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author dereeper
date Tue, 12 Apr 2016 09:31:56 -0400
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1 <tool id="admixture" name="Admixture" version="1.23">
2 <description>a population structure from large SNP genotype datasets</description>
3 <requirements>
4 <requirement type="package" version="1.23">admixture</requirement>
5 </requirements>
6 <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax
7 </command>
8 <inputs>
9 <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/>
10 <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/>
11 <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/>
12 <param type="text" name="kmin" label="K min" value="2"/>
13 <param type="text" name="kmax" label="K max" value="5"/>
14 </inputs>
15 <outputs>
16 <data format="txt" name="best_k_output" label="Best K Output"/>
17 <data format="txt" name="best_k_logfile" label="Best K Logfile"/>
18 <data format="txt" name="outputs" label="All Outputs"/>
19 <data format="txt" name="logs" label="All Logs"/>
20 </outputs>
21
22 <tests>
23 <test>
24 <param name="bed" value="input.bed" />
25 <param name="bim" value="input.bim" />
26 <param name="fam" value="input.fam" />
27 <param name="kmax" value="3" />
28
29 <output name="best_k_output" file="output" />
30 <output name="outputs" file="outputs.Q" />
31 </test>
32
33 </tests>
34
35 <help>
36
37
38 .. class:: infomark
39
40 **Program encapsulated in Galaxy by Southgreen**
41
42 .. class:: infomark
43
44 **Admixture version 1.23**
45
46 -----
47
48 ==============
49 Please cite:
50 ==============
51
52 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.
53
54 -----
55
56
57 ===========
58 Overview:
59 ===========
60
61 ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).
62
63 -----
64
65 For further informations, please visite the Admixture_ website.
66
67
68 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
69 </help>
70
71 <citations>
72 <citation type="doi" >10.1101/gr.094052.109</citation>
73 </citations>
74
75
76
77 </tool>