Mercurial > repos > dereeper > mlmm
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author | dereeper |
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date | Thu, 02 Jul 2015 05:42:38 -0400 |
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<tool id="mlmm" name="MLMM" version="1.0"> <description>GWAS using Multi-Locus Mixed-Model (MLMM)</description> <requirements> <requirement type="binary">Rscript</requirement> </requirements> <command interpreter="bash">./MLMM.sh $geno $map $pheno $steps $method $output $pdf $kinship $rss $step_table $log </command> <inputs> <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"/> <param type="data" format="txt" name="map" label="SNP Information file" help="3 columns: SNP, Chrom, Pos"/> <param format="txt" name="pheno" type="data" label="Phenotype matrix" help="NxT, N = individuals in line, T = Trait in columns (Phenot1, Phenot2...)"/> <param type="text" name="steps" label="Maximum number of steps for the forward approach" value="10"/> <param name="method" type="select"> <option value="extBIC">EBIC</option> <option value="mbonf" selected="True">MBonf</option> </param> </inputs> <outputs> <data format="txt" name="output" label="Association results"/> <data format="txt" name="kinship" label="Kinship matrix"/> <data format="pdf" name="pdf" label="PDF Graphical outputs"/> <data format="txt" name="rss" label="RSS"/> <data format="txt" name="step_table" label="Step Table"/> <data format="txt" name="log" label="Log file"/> </outputs> <help> .. class:: infomark **Program encapsulated in Galaxy by Southgreen** .. class:: infomark **MLMM version 1.0** ----- ============== 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. ----- =========== Overview: =========== MLMM is an efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. ----- For further informations, please visite the MLMM_ website. .. _MLMM: https://sites.google.com/site/vincentosegura/mlmm </help> </tool>