--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EstimEndem.xml	Tue May 20 09:52:29 2025 +0000
@@ -0,0 +1,246 @@
+<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>