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+++ b/mlmm/MLMM.xml	Thu Jul 02 05:42:38 2015 -0400
@@ -0,0 +1,61 @@
+<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>