annotate hyphy_fel.xml @ 2:a8b34daec0d9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"

<?xml version="1.0"?>
<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0">
    <description>Fixed Effects Likelihood</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' fel_input.fa &&
        ln -s '$input_nhx' fel_input.nhx &&
        @HYPHY_INVOCATION@ fel
            --alignment ./fel_input.fa
            --tree ./fel_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --srv '$include_srv'
            --pvalue '$p_value'
            > '$fel_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="include_srv" type="select" label="Include synonymous rate variation">
            <option value="Yes">Yes (recommended)</option>
            <option value="No">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="fel_log" format="txt"/>
        <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.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="fel_output" file="fel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method 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/#fel
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msi105</citation>
    </expand>
</tool>