<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1">
    <description>Mixed Effects Model of Evolution</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' meme_input.fa &&
        ln -s '$input_nhx' meme_input.nhx &&
        @HYPHYMPI@ meme
            --alignment ./meme_input.fa
            --tree ./meme_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            --output '$meme_output'
            > '$meme_log'
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>
        <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
    </inputs>
    <outputs>
        <data name="meme_log" format="txt"/>
        <data name="meme_output" format="hyphy_results.json" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
            <param name="branches" value="All"/>
            <param name="p_value" value="0.1"/>
            <output name="meme_output" file="meme-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#meme
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pgen.1002764</citation>
    </expand>
</tool>