<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1">
    <description>Single Likelihood Ancestor Counting</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' slac_input.fa &&
        ln -s '$input_nhx' slac_input.nhx &&
        hyphy slac
            --alignment ./slac_input.fa
            --tree ./slac_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --samples '$number_of_samples'
            --pvalue '$p_value'
            --output '$slac_output'
        > '$slac_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"/>
        <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
    </inputs>
    <outputs>
        <data name="slac_log" format="txt"/>
        <data name="slac_output" format="hyphy_results.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="slac_output" file="slac-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny.

See the online documentation_ for more information.

.. _documentation: http://hyphy.org/methods/selection-methods/#slac
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msi105</citation>
    </expand>
</tool>