annotate hyphy_busted.xml @ 0:edabb77ac0d4 draft

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

<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0">
    <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
    <![CDATA[
    ln -s '$input_file' busted_input.fa &&
    ln -s '$input_nhx' busted_input.nhx &&
    echo $gencodeid > tool_params &&
    echo `pwd`/busted_input.fa >> tool_params &&
    echo `pwd`/busted_input.nhx >> tool_params &&
    echo '$branches' >> tool_params &&
    @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf > '$busted_log'
    ]]>
    </command>
    <inputs>
        <expand macro="inputs" />
        <expand macro="gencode" />
        <expand macro="branches" />
    </inputs>
    <outputs>
        <data name="busted_log" format="txt" />
        <data name="busted_output" format="json" from_work_dir="busted_input.fa.BUSTED.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="busted_output" file="busted-out1.json" compare="sim_size" />
        </test>
    </tests>
    <help>
        <![CDATA[
BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.
        ]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv035</citation>
    </expand>
</tool>