<tool id="Beagle" name="Beagle4.0" >
  <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="python">

    #if int($useref.refSelect)==0
      beagle4.py --jar $__tool_directory__/beagle.r1399.jar --gtgl $gtORgl.gtORglSelect --gfile $gtORgl.gtgl --phase-its $phaseits --impute-its $imputeits  --out $output
    #else
      beagle4.py --jar $__tool_directory__/beagle.r1399.jar --gtgl $gtORgl.gtORglSelect --gfile $gtORgl.gtgl --ref $useref.ref --phase-its $phaseits --impute-its $imputeits --out $output
    #end if


  </command>

<inputs>

<conditional name="useref">

    <param name="refSelect" type="select" label="Select to use a reference or to estimate phasing">
      <option value="1" selected="true">Reference</option>
      <option value="0" >Estimate</option>
    </param>

    <when value="1">
      <param format="vcf" name="ref" type="data" label="Reference file" help="ref=[file] specifies a reference VCF file containing additional samples and phased genotypes for each marker. See also the impute parameter." />
    </when>
</conditional>

<conditional name="gtORgl">
  <param name="gtORglSelect" type="select" label="Select genotype or genotype likelihood input file" help="Either file option requires VCF format">
    <option value="gt" selected="true">Genotype</option>
    <option value="gl">Genotype Likelihood</option>
  </param>
  <when value="gt">
    <param format="vcf" name="gtgl" type="data" label="GT file" help="gt=[file] specifies a VCF file containing a GT (genotype) format field for each marker."/>
  </when>
  <when value="gl">
    <param format="vcf" name="gtgl" type="data" label="GL file" help="gl=[file] specifies a VCF file containing a GL or PL (genotype likelihood) format field for each marker. If both GL and PL format fields are present for a sample, the GL format will be used. See also the maxlr parameter." />
  </when>
</conditional>

  <param name="imputeits" type="integer" size="3" value="5" label="Impute-ITS (iterations for impute step: default=5)" help="" />
  <param name="phaseits" type="integer" size="3" value="5" label="Phase-ITS (iterations for phase step: default=5)" />

</inputs>

<outputs>
  <data format="vcf" name="output" label="Output from Beagle" />

</outputs>


<help>

For a full guide, go to the Beagle4.0 documentation here: http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf

This wrapper allows for the selection of either a Genotype (gt) file, a Genotype Likelihood (gl) file or a Genotype (gt) plus Reference file as per the example usage here: http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example

The only parameters currently exposed by this wrapper are impute-its and phase-its which both have default of 5. Please feel free to request more parameters to be made available by contacting bobbledavidson @ github.

Test data is available via the GitHub page: https://github.com/bobbledavidson/Beagle4Galaxy

Important note:
The creator of the Galaxy wrapper is not the same as the creator of the Beagle4.0 tool. All credit for the tool's abilities should be acknowledged using the following citation:

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. doi:10.1086/521987

</help>



</tool>