<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
    <description>adaptive Branch Site Random Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' absrel_input.fa &&
        ln -s '$input_nhx' absrel_input.nhx &&
        @HYPHY_INVOCATION@ absrel
            --alignment ./absrel_input.fa
            --tree ./absrel_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            > '$absrel_log'
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
    </inputs>
    <outputs>
        <data name="absrel_log" format="txt">
            <filter>log</filter>
        </data>
        <data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#absrel
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>
</tool>