comparison admixture/admixture.xml @ 21:50bd37c444ac draft

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author dereeper
date Mon, 23 Mar 2015 05:35:48 -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="1.07">plink</requirement>
5 <requirement type="package" version="1.23">admixture</requirement>
6 </requirements>
7 <command interpreter="bash">./admixture.sh $input $outputs $logs $best_k_output $best_k_logfile $kmin $kmax
8 </command>
9 <inputs>
10 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
11 <param type="text" name="kmin" label="K min" value="1"/>
12 <param type="text" name="kmax" label="K max" value="5"/>
13 </inputs>
14 <outputs>
15 <data format="txt" name="best_k_output" label="Best K Output"/>
16 <data format="txt" name="best_k_logfile" label="Best K Logfile"/>
17 <data format="txt" name="outputs" label="All Outputs"/>
18 <data format="txt" name="logs" label="All Logs"/>
19 </outputs>
20 <help>
21
22
23 .. class:: infomark
24
25 **Program encapsulated in Galaxy by Southgreen**
26
27 .. class:: infomark
28
29 **Admixture version 1.23**
30
31 -----
32
33 ==============
34 Please cite:
35 ==============
36
37 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.
38
39 -----
40
41 ===========
42 Overview:
43 ===========
44
45 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).
46
47 -----
48
49 For further informations, please visite the Admixture_ website.
50
51
52 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
53 </help>
54
55 </tool>