<tool id="mlmm" name="MLMM (GWAS analysis)" version="2.0.0">
	<description>GWAS using Multi-Locus Mixed-Model (MLMM)</description>
	<requirements>
		<requirement type="binary">Rscript</requirement>
                <requirement type="binary">perl</requirement>
                <requirement type="package" version="1.6.924">perl-bioperl</requirement>
	</requirements>
        <stdio>
            <exit_code range="1:" level="fatal" />
        </stdio>
	<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>
        <tests>
            <test>
                <param name="geno" value="genot.txt"/>
                <param name="map" value="map.txt"/>
                <param name="pheno" value="phenot.txt"/>
                <param name="steps" value="10"/>
                <param name="method" value="mbonf"/>
                <output name="output" value="output.txt"/>
                <output name="kinship" value="kinship.txt"/>
                <output name="rss" value="rss.txt"/>
                <output name="step_table" value="step_table.txt"/>
            </test>
        </tests>
	<help><![CDATA[


.. 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.

.. class:: infomark

**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

---------------------------------------------------

====
MLMM
====

-----------
Description
-----------
 
  | 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_.


.. _website: https://sites.google.com/site/vincentosegura/mlmm

------------
Dependencies
------------
MLMM
        mlmm 1.0, Based on a archive provide by Vincent Segura: https://sites.google.com/site/vincentosegura/mlmm
Bioperl
        perl-bioperl_ 1.6.924, Conda version

.. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl

        ]]></help>
        <citations>
            <citation type="doi">10.1038/ng.2314</citation>
        </citations>
</tool>