annotate hyphy_fel.xml @ 0:24a2bf70dbdd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea

<?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" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
    ln -s '$input_file' fel_input.fa &&
    ln -s '$input_nhx' fel_input.nhx &&
    echo $gencodeid > tool_params &&
    echo `pwd`/fel_input.fa >> tool_params &&
    echo `pwd`/fel_input.nhx >> tool_params &&
    echo '$branches' >> tool_params &&
    echo '$include_srv' >> tool_params &&
    echo '$p_value' >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$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="1">Yes (recommended)</option>
            <option value="2">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="fel_log" format="txt" />
        <data name="fel_output" format="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.
        ]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msi105</citation>
    </expand>
</tool>