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author ecology
date Thu, 22 May 2025 16:43:50 +0000
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1 <tool id="phylo_index" name="PhyloIndex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>compute phylodiversity index based on matched phylogenetic and occupancy data</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">1.0</token>
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 </macros>
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9 <requirements>
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10 <requirement type="package" version="1.0.8">r-phyloregion</requirement>
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11 <requirement type="package" version="1.6.5">r-matrix</requirement>
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12 <requirement type="package" version="5.8_1">r-ape</requirement>
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13 <requirement type="package" version="1.2.2">bioconductor-sparsearray</requirement>
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14 </requirements>
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16 <required_files>
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17 <include path="PhyloIndex.R" />
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18 </required_files>
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21 <command detect_errors="exit_code">
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22 <![CDATA[
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23 Rscript '$__tool_directory__/PhyloIndex.R'
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24 '$phylogeny'
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25 '$occupancy'
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26 '$random_seed'
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27 '$model'
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28 '$output'
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29 ]]>
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30 </command>
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32 <inputs>
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33 <param name="phylogeny" type="data" format="newick" label="Phylogeny file (Newick format)" />
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34 <param name="occupancy" type="data" format="tabular" label="Occupancy data (Tabular format)" />
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35 <param name="random_seed" type="integer" value="34" label="Seed for the random PD compute"/>
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36 <param name="model" type="select" label="Model for the PD compute">
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37 <option value="tipshuffle" selected="true">tipshuffle</option>
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38 <option value="rowwise">rowwise</option>
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39 <option value="colwise">colwise</option>
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <data name ="output" format="tabular" label="a table" />
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="phylogeny" value="tree_file"/>
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49 <param name="occupancy" value="matrix_file"/>
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50 <param name="random_seed" value="34"/>
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51 <param name="model" value="tipshuffle"/>
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52 <output name="output" file="output" ftype="tabular"/>
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53 </test>
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54 </tests>
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55
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56 <help><![CDATA[
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57 this tool computes the phylodiversity index based on matched phylogenetic and occupancy data using the R script PhyloIndex.R.
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58 Ensure that the input files are in the correct formats:
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59 - Phylogeny file: Newick format
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60 - Occupancy data: Tabular format
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61 The output will be a tabular file containing the computed phylodiversity index.
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62 ]]></help>
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63
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64 <citations>
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65 <citation type="doi">10.32614/CRAN.package.phyloregion</citation>
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66 <citation type="doi">10.32614/CRAN.package.Matrix</citation>
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67 <citation type="doi">10.32614/CRAN.package.ape</citation>
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68 <citation type="doi">10.18129/B9.bioc.SparseArray</citation>
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69 </citations>
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70 </tool>