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<tool id="Beagle" name="Beagle" version="1.0.0" >
	<description>Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection</description>
	<requirements>
		<requirement type="package" version="4.0">Beagle</requirement>
	</requirements>
	<command interpreter="bash">$__tool_directory__/execute_beagle.sh $vcf_input $phase $impute</command>
	<inputs>
		<param format="vcf" name="vcf_input" type="data" label="Variant call format"/>
		<param type="text" name="phase" value="5" help="Non-negative integer" label="specifies the number of iterations for estimating genotype phase (default: phase-its=5).Increasing this parameter will typicall increase genotype phaseaccuracy."/>
		<param type="text" name="impute" value="5" help="Non-negative integer" label="specifies the number of iterations for estimating genotypes at ungenotyped markers (default:impute-its=5). Increasing this parameter (up to ~10 iterations) will typically increase genotype imputation accuracy."/>
	</inputs>
	<outputs>
		<data format="vcf" name="vcf_ouput" label="Phased and imputed VCF" from_work_dir="out.vcf"/>
		<data format="txt" name="log" label="Beagle log file" from_work_dir="out.log"/>
	</outputs>

	<!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
	<tests>
	<!-- [HELP] Test files have to be in the ~/test-data directory -->
		<test>
			<param name="vcf_input" value="Annotated_VCF.vcf" />
			<param name="phase" value="5" />
			<param name="impute" value="5" />
			<output name="vcf_ouput" file="output.vcf" compare="sim_size"/>
			<output name="log" file="filelog.txt" compare="sim_size"/>
		</test>
	</tests>
	<help><![CDATA[



.. class:: infomark

**Beagle** version 4 
 |  **If you use Beagle in a published analysis, please report the program version and cite the following article** "S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-97."

.. class:: infomark

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

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]

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

======
Beagle
======

-----------
Description
-----------

  |  Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Version 4 has multiple improvements:

    a standard format (Variant Call Format) for input and output files
    a powerful identity by descent detection algorithm: Refined IBD
    support for multi-threaded computation
    support for multi-allelic markers
    improved methods for phasing and genotype imputation
    elimination of temporary files
    use of a sliding window permit control memory use

  | For further informations, please visite the Beagle website_.


.. _website: https://faculty.washington.edu/browning/beagle/b4_0.html


	]]></help>
        <citations>
            <citation type="doi">10.1086/521987</citation>
        </citations>

</tool>