<?xml version="1.0"?>
<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
    <description>Genetic Algorithm for Recombination Detection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' gard_input.fa &&
        @HYPHYMPI@ gard
            --alignment ./gard_input.fa
            --type '$datatype.value'
            #if str($datatype.value) == 'Codon':
                --code '$datatype.gencodeid'
            #elif str($datatype.value) == 'Protein':
                --model '$datatype.model'
            #end if
            --rv '$rate_cond.rate'
            #if str($rate_cond.rate) != 'None':
                --rate-classes '$rate_classes'
            #end if
            --output '$translated'
            --output-lf '$gard_output'
            > '$gard_log'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
        <conditional name="datatype">
            <param name="value" type="select" label="Type of data">
                <option value="nucleotide">Nucleotide</option>
                <option value="protein">Amino acid</option>
                <option value="codon">Codon</option>
            </param>
            <when value="Nucleotide"/>
            <when value="Protein">
                <expand macro="substitution" />
            </when>
            <when value="Codon">
                <expand macro="gencode" />
            </when>
        </conditional>
        <conditional name="rate_cond">
            <param name="rate" type="select" label="Rate variation">
                <option value="None">None</option>
                <option value="GDD">General Discrete</option>
                <option value="Gamma">Beta-Gamma</option>
            </param>
            <when value="None"/>
            <when value="GDD">
                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
            </when>
            <when value="Gamma">
                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="gard_log" format="txt"/>
        <data name="gard_output" format="nex" />
        <data name="translated" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
            <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
        </test>
    </tests>
    <help><![CDATA[
GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#gard
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msl051</citation>
    </expand>
</tool>