<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
    <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' busted_input.fa &&
        ln -s '$input_nhx' busted_input.nhx &&
        @HYPHY_INVOCATION@ busted
            --alignment ./busted_input.fa
            --tree ./busted_input.nhx
            --code $gencodeid
            --branches '$branches'
            > '$busted_log'
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
    </inputs>
    <outputs>
        <data name="busted_log" format="txt"/>
        <data name="busted_output" format="hyphy_results.json" from_work_dir="busted_input.fa.BUSTED.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
            <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#busted
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv035</citation>
    </expand>
</tool>