view PhyloIndex.xml @ 1:1d73a4af71f5 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit ce74877d21915627f36eae4d2eb3851a6a858aae

<tool id="phylo_index" name="PhyloIndex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>compute phylodiversity index based on matched 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="PhyloIndex.R" />
    </required_files>


    <command detect_errors="exit_code">
        <![CDATA[
        Rscript '$__tool_directory__/PhyloIndex.R' 
            '$phylogeny'  
            '$occupancy' 
            '$random_seed'
            '$model'
            '$output' 
        ]]> 
    </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)" />
        <param name="random_seed" type="integer" value="34" label="Seed for the random PD compute"/>
        <param name="model" type="select" label="Model for the PD compute">
            <option value="tipshuffle" selected="true">tipshuffle</option>
            <option value="rowwise">rowwise</option>
            <option value="colwise">colwise</option>
        </param>
    </inputs>
    <outputs>
        <data name ="output" format="tabular" label="a table" />
    </outputs>

    <tests>
        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="random_seed" value="34"/>
            <param name="model" value="tipshuffle"/>
            <output name="output" file="output" ftype="tabular"/>
        </test>
    </tests>

    <help><![CDATA[
    this tool computes the phylodiversity index based on matched phylogenetic and occupancy data using the R script PhyloIndex.R.
    Ensure that the input files are in the correct formats:
    - Phylogeny file: Newick format
    - Occupancy data: Tabular format
    The output will be a tabular file containing the computed phylodiversity index.
    ]]></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>