<?xml version="1.0"?>
<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0">
    <description>Detect relaxed selection in a codon-based
    phylogenetic framework</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' relax_input.fa &&
        ln -s '$input_nhx' relax_input.nhx &&
        hyphy relax
            --alignment ./relax_input.fa
            --tree ./relax_input.nhx
            --models '$analysisType'
            #if $treeAnnotations == "2":
                --test TEST
                --reference REFERENCE
            #else:
                --test TEST
            #end if
            > '$relax_log'
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param name="analysisType" type="select" label="Analysis Type">
            <option value="All">All</option>
            <option value="Minimal">Minimal</option>
        </param>
        <param name="treeAnnotations" type="select" label="Tree Annotations">
            <option value="1">TEST only</option>
            <option value="2">TEST and REFERENCE</option>
        </param>
    </inputs>
    <outputs>
        <data name="relax_log" format="txt"/>
        <data name="relax_output" format="hyphy_results.json" from_work_dir="relax_input.fa.RELAX.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>
            <output name="relax_output" file="relax-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
RELAX is a hypothesis testing framework that asks whether the strength of natural selection has been relaxed or intensified along a specified set of test branches. RELAX is therefore not a suitable method for explicitly testing for positive selection. Instead, RELAX is most useful for identifying trends and/or shifts in the stringency of natural selection on a given gene.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#relax
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msu400</citation>
    </expand>
</tool>