diff PhylOccuMatcher.xml @ 0:e260f1a598da draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PhylOccuMatcher.xml	Tue May 20 09:53:38 2025 +0000
@@ -0,0 +1,64 @@
+<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>