<tool id="phylogenetic_occupancy_matcher" name="PhylOccuMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>match phylogenetic and occupancy data</description>
    
    <macros>
        <token name="@TOOL_VERSION@">1.0</token> 
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    
    <requirements> 
        <requirement type="package" version="1.0.8">r-phyloregion</requirement>
        <requirement type="package" version="1.6.5">r-matrix</requirement>
        <requirement type="package" version="5.8_1">r-ape</requirement>
        <requirement type="package" version="1.2.2">bioconductor-sparsearray</requirement>
    </requirements>

    <required_files>
        <include path="PhylOccuMatcher.R" />
    </required_files>


    <command>
        <![CDATA[
        Rscript '$__tool_directory__/PhylOccuMatcher.R' 
            '$phylogeny' 
            '$occupancy'
            '$output1' 
            '$output2'
        ]]>
    </command>

    <inputs>
        <param name="phylogeny" type="data" format="newick" label="Phylogeny file (Newick format)" />
        <param name="occupancy" type="data" format="tabular" label="Occupancy data (Tabular format)" />
    </inputs>
    <outputs>
        <data name="output1" format="newick" label="Phylogeny with occupancy data" />
        <data name="output2" format="tabular" label="Matched output data" />
    </outputs>
    
    <tests>
        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="actinos_test"/>
            <output name="output1" file="output1" ftype="newick"/>
            <output name="output2" file="output2" ftype="tabular"/>
        </test>
    </tests>

    <help>
        <![CDATA[
        This tool matches phylogenetic data with occupancy data using a phylogeny file and an occupancy file.
        Ensure that the input files are in the correct formats:
        - Phylogeny file: Newick format
        - Occupancy data: Tabular format
        ]]>
    </help>

    <citations>
        <citation type="doi">10.32614/CRAN.package.phyloregion</citation>
        <citation type="doi">10.32614/CRAN.package.Matrix</citation>
        <citation type="doi">10.32614/CRAN.package.ape</citation>
        <citation type="doi">10.18129/B9.bioc.SparseArray</citation>
    </citations>
</tool>