annotate admixture/.svn/text-base/admixture.xml.svn-base @ 24:21d878747ac6 draft default tip

Uploaded
author dereeper
date Mon, 23 Mar 2015 05:53:20 -0400
parents 13cff72ec2d3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
1 <tool id="admixture" name="Admixture" version="1.23">
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
2 <description>a population structure from large SNP genotype datasets</description>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
3 <requirements>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
4 <requirement type="package" version="1.07">plink</requirement>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
5 <requirement type="package" version="1.23">admixture</requirement>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
6 </requirements>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
7 <command interpreter="bash">./admixture.sh $input $outputs $logs $best_k_output $best_k_logfile $kmin $kmax
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
8 </command>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
9 <inputs>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
10 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
11 <param type="text" name="kmin" label="K min" value="1"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
12 <param type="text" name="kmax" label="K max" value="5"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
13 </inputs>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
14 <outputs>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
15 <data format="txt" name="best_k_output" label="Best K Output"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
16 <data format="txt" name="best_k_logfile" label="Best K Logfile"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
17 <data format="txt" name="outputs" label="All Outputs"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
18 <data format="txt" name="logs" label="All Logs"/>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
19 </outputs>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
20 <help>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
21
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
22
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
23 .. class:: infomark
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
24
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
25 **Program encapsulated in Galaxy by Southgreen**
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
26
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
27 .. class:: infomark
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
28
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
29 **Admixture version 1.23**
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
30
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
31 -----
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
32
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
33 ==============
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
34 Please cite:
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
35 ==============
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
36
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
37 "Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
38
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
39 -----
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
40
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
41 ===========
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
42 Overview:
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
43 ===========
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
44
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
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).
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
46
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
47 -----
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
48
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
49 For further informations, please visite the Admixture_ website.
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
50
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
51
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
52 .. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
53 </help>
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
54
13cff72ec2d3 Uploaded
dereeper
parents:
diff changeset
55 </tool>