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<tool id="admixture" name="Admixture" version="1.23">
	<description>a population structure from large SNP genotype datasets</description>
	<requirements>
		<requirement type="package" version="1.23">admixture</requirement>
	</requirements>
	<command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax $best_k_groups $threshold_group
    </command>
	<inputs>
		<param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/>
		<param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/>
		<param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/>
		<param type="text" name="kmin" label="K min" value="2"/>
		<param type="text" name="kmax" label="K max" value="5"/>
		<param type="text" name="threshold_group" label="Minimum admixture proportion percentage for group assignation" value="50"/>
	</inputs>
	<outputs>
		<data format="txt" name="best_k_output" label="Best K Output"/>
		<data format="txt" name="best_k_groups" label="Best K Groups"/>
		<data format="txt" name="best_k_logfile" label="Best K Logfile"/>
		<data format="txt" name="outputs" label="All Outputs"/>
		<data format="txt" name="logs" label="All Logs"/>
	</outputs>

	<tests>
		<test>
			<param name="bed" value="input.bed" />
			<param name="bim" value="input.bim" />
			<param name="fam" value="input.fam" />
			<param name="kmax" value="3" />
			<param name="threshold_group" value="60" />
			<output name="best_k_output" file="output" />
			<output name="outputs" file="outputs.Q" />
			<output name="best_k_groups" file="groups" />
		</test>

	</tests>

	<help>
	

.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**

.. class:: infomark

**Admixture version 1.23**

-----

==============
 Please cite: 
==============

"Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.

-----

===========
 Overview:
===========

ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).

-----

For further informations, please visite the Admixture_ website.


.. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
	</help>
<citations>
<citation type="doi" >10.1101/gr.094052.109</citation>
</citations>
</tool>