Mercurial > repos > dereeper > mlmm

comparison MLMM.xml @ 1:380b364980f9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:50:05 -0400
parents
children
comparison
equal deleted inserted replaced
0:6b7107812931 1:380b364980f9
1 <tool id="mlmm" name="MLMM (GWAS analysis)" version="2.0.0">
2 <description>GWAS using Multi-Locus Mixed-Model (MLMM)</description>
3 <requirements>
4 <requirement type="binary">Rscript</requirement>
5 <requirement type="binary">perl</requirement>
6 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" level="fatal" />
10 </stdio>
11 <command interpreter="bash">./MLMM.sh $geno $map $pheno $steps $method $output $pdf $kinship $rss $step_table $log</command>
12 <inputs>
13 <param format="txt" name="geno" type="data" label="Genotype matrix" help="NxM, N = individuals in line, M = Markers in columns, Genotype coded in 0,1,2"/>
14 <param type="data" format="txt" name="map" label="SNP Information file" help="3 columns: SNP, Chrom, Pos"/>
15 <param format="txt" name="pheno" type="data" label="Phenotype matrix" help="NxT, N = individuals in line, T = Trait in columns (Phenot1, Phenot2...)"/>
16 <param type="text" name="steps" label="Maximum number of steps for the forward approach" value="10"/>
17 <param name="method" type="select">
18 <option value="extBIC">EBIC</option>
19 <option value="mbonf" selected="True">MBonf</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data format="txt" name="output" label="Association results"/>
24 <data format="txt" name="kinship" label="Kinship matrix"/>
25 <data format="pdf" name="pdf" label="PDF Graphical outputs"/>
26 <data format="txt" name="rss" label="RSS"/>
27 <data format="txt" name="step_table" label="Step Table"/>
28 <data format="txt" name="log" label="Log file"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="geno" value="genot.txt"/>
33 <param name="map" value="map.txt"/>
34 <param name="pheno" value="phenot.txt"/>
35 <param name="steps" value="10"/>
36 <param name="method" value="mbonf"/>
37 <output name="output" value="output.txt"/>
38 <output name="kinship" value="kinship.txt"/>
39 <output name="rss" value="rss.txt"/>
40 <output name="step_table" value="step_table.txt"/>
41 </test>
42 </tests>
43 <help><![CDATA[
44
45
46 .. class:: infomark
47
48 **MLMM** version 1.0
49 | **Please cite** "An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.", **Segura V, Vilhjalmsson BJ, Platt A, Korte A, Seren U, Long Q, Nordborg M.**, Nature Genetics, 44: 825-830, 2012.
50
51 .. class:: infomark
52
53 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
54
55 .. class:: infomark
56
57 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
58
59 ---------------------------------------------------
60
61 ====
62 MLMM
63 ====
64
65 -----------
66 Description
67 -----------
68
69 | MLMM is an efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.
70 | For further informations, please visite the MLMM website_.
71
72
73 .. _website: https://sites.google.com/site/vincentosegura/mlmm
74
75 ------------
76 Dependencies
77 ------------
78 MLMM
79 mlmm 1.0, Based on a archive provide by Vincent Segura: https://sites.google.com/site/vincentosegura/mlmm
80 Bioperl
81 perl-bioperl_ 1.6.924, Conda version
82
83 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
84
85 ]]></help>
86 <citations>
87 <citation type="doi">10.1038/ng.2314</citation>
88 </citations>
89 </tool>