<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0">
    <description>Single Likelihood Ancestor Counting</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
    ln -s '$input_file' slac_input.fa &&
    ln -s '$input_nhx' slac_input.nhx &&
    echo $gencodeid > tool_params &&
    echo `pwd`/slac_input.fa >> tool_params &&
    echo `pwd`/slac_input.nhx >> tool_params &&
    echo '$branches' >> tool_params &&
    echo '$number_of_samples' >> tool_params &&
    echo '$p_value' >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/SLAC.bf > '$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="json" from_work_dir="slac_input.fa.SLAC.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.
        ]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msi105</citation>
    </expand>
</tool>