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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
author ecology
date Tue, 20 May 2025 09:52:29 +0000
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children f3a977826375
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<tool id="estimate_endem" name="EstimEndem" version="0.1.0+galaxy0" profile="21.05">
    <description>
        of each cell of a spatial grid
    </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>
        <requirement type="package" version="1.0_20">r-sf</requirement>
        <requirement type="package" version="2.2_0">r-sp</requirement>
        <requirement type="package" version="3.6_32">r-raster</requirement>
        <requirement type="package" version="1.1.4">r-dplyr</requirement> 
    </requirements>

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


    <command detect_errors="exit_code">
        <![CDATA[
        mkdir '$shapefile.extra_files_path' &&
        Rscript '$__tool_directory__/EstimEndem.R'
            '$phylogeny'  
            '$occupancy'
            ${os.path.join( $coordinates_file_input.extra_files_path, "shapefile.shp" )} 
            '$nb_cluster'
            '$clustering_method'
            
        &&
        mv output.* '${shapefile.extra_files_path}'

        ]]>
    </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 ="coordinates_file_input" type="data" format="shp" label="input_shapefile" help="Provide coordinates files"/>
        <param name="nb_cluster" type="integer" value="10" label="the number of cluster" help="choose the number of phyloregion"/>
        <param name ="clustering_method" type="select" checked="true" 
               label="Choose a clustering method" help="choose">
            <option value="ward.D" selected="true">ward.D</option>
            <option value="ward.D2">ward.D2</option>
            <option value="single">single</option>
            <option value="complete">complete</option>
            <option value="average">UPGMA</option>
            <option value="mcquitty">WPGMA</option>
            <option value="median">WPGMC</option>
            <option value="centroid">UPGMC</option>
        </param>

    </inputs>
    <outputs>
        <data name="shapefile" format="shp" label="shapefile"/>
    </outputs>

    <tests>
        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="ward.D"/>

            <output file="shapefile_out_1/shapefile_shp_test1.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_1/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_1/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_1/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_1/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="ward.D2"/>

            <output file="shapefile_out_2/shapefile_shp_test2.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_2/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_2/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_2/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_2/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="single"/>

            <output file="shapefile_out_3/shapefile_shp_test3.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_3/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_3/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_3/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_3/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="complete"/>

            <output file="shapefile_out_4/shapefile_shp_test4.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_4/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_4/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_4/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_4/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="average"/>

            <output file="shapefile_out_5/shapefile_shp_test5.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_5/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_5/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_5/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_5/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="mcquitty"/>

            <output file="shapefile_out_6/shapefile_shp_test6.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_6/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_6/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_6/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_6/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="median"/>

            <output file="shapefile_out_7/shapefile_shp_test7.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_7/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_7/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_7/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_7/output.prj"/>
            </output>
        </test>

        <test>
            <param name="phylogeny" value="tree_file"/>
            <param name="occupancy" value="matrix_file"/>
            <param name="coordinates_file_input" value="composite_dataset/shapefile" ftype="shp">
                <composite_data value="composite_dataset/shapefile.shp"/>
                <composite_data value="composite_dataset/shapefile.shx"/>
                <composite_data value="composite_dataset/shapefile.dbf"/>
                <composite_data value="composite_dataset/shapefile.prj"/>
            </param>
            <param name="nb_cluster" value="8"/>
            <param name="clustering_method" value="centroid"/>

            <output file="shapefile_out_8/shapefile_shp_test8.html" name="shapefile">
                <extra_files type="file" name="output.shp" value="shapefile_out_8/output.shp"/>
                <extra_files type="file" name="output.shx" value="shapefile_out_8/output.shx"/>
                <extra_files type="file" name="output.dbf" value="shapefile_out_8/output.dbf" compare="sim_size" delta="50"/>
                <extra_files type="file" name="output.prj" value="shapefile_out_8/output.prj"/>
            </output>
        </test>
    </tests>

    <help>
        <![CDATA[
            This tool estimates the endemism of each cell in a spatial grid using the provided phylogeny, occupancy data, and spatial coordinates. 
            Ensure that the input files are in the correct formats: Newick for phylogeny, tabular for occupancy, and shapefile for spatial data.

        ]]>
    </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>
        <citation type="doi">10.32614/CRAN.package.sf</citation>
        <citation type="doi">10.32614/CRAN.package.sp</citation>
        <citation type="doi">10.32614/CRAN.package.raster</citation>
        <citation type="doi">10.32614/CRAN.package.dplyr</citation>
    </citations>
    
</tool>