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1 <tool id="mlmm" name="MLMM" version="1.0">
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2 <description>GWAS using Multi-Locus Mixed-Model (MLMM)</description>
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3 <requirements>
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4 <requirement type="binary">Rscript</requirement>
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5 </requirements>
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6 <command interpreter="bash">./MLMM.sh $geno $map $pheno $steps $method $output $pdf $kinship $rss $step_table $log
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7 </command>
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8 <inputs>
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9 <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"/>
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10 <param type="data" format="txt" name="map" label="SNP Information file" help="3 columns: SNP, Chrom, Pos"/>
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11 <param format="txt" name="pheno" type="data" label="Phenotype matrix" help="NxT, N = individuals in line, T = Trait in columns (Phenot1, Phenot2...)"/>
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12 <param type="text" name="steps" label="Maximum number of steps for the forward approach" value="10"/>
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13 <param name="method" type="select">
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14 <option value="extBIC">EBIC</option>
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15 <option value="mbonf" selected="True">MBonf</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="output" label="Association results"/>
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20 <data format="txt" name="kinship" label="Kinship matrix"/>
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21 <data format="pdf" name="pdf" label="PDF Graphical outputs"/>
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22 <data format="txt" name="rss" label="RSS"/>
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23 <data format="txt" name="step_table" label="Step Table"/>
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24 <data format="txt" name="log" label="Log file"/>
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25 </outputs>
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26 <help>
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27
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28
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29 .. class:: infomark
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30
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31 **Program encapsulated in Galaxy by Southgreen**
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32
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33 .. class:: infomark
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34
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35 **MLMM version 1.0**
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36
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37 -----
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38
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39 ==============
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40 Please cite:
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41 ==============
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42
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43 "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.
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44
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45 -----
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46
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47 ===========
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48 Overview:
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49 ===========
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50
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51 MLMM is an efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.
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52
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53 -----
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54
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55 For further informations, please visite the MLMM_ website.
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56
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57
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58 .. _MLMM: https://sites.google.com/site/vincentosegura/mlmm
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59 </help>
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60
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61 </tool>
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