Mercurial > repos > iuc > phyloseq_plot_ordination

annotate phyloseq_plot_ordination.xml @ 0:11d43fa12aab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author iuc
date Thu, 03 Mar 2022 13:28:30 +0000
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children 92e77800ef2c
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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1 <tool id="phyloseq_plot_ordination" name="Phyloseq: plot ordination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '${__tool_directory__}/phyloseq_plot_ordination.R'
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9 --input '$input'
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10 --method '$method'
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11 --distance '$distance'
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12 --type '$type'
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13 --output '$output'
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14 ]]></command>
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15 <inputs>
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16 <expand macro="phyloseq_input"/>
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17 <param name="method" type="select" label="Ordination method">
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18 <option value="DCA" selected="true">DCA</option>
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19 <option value="CCA">CCA</option>
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20 <option value="RDA">RDA</option>
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21 <option value="CAP">CAP</option>
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22 <option value="NMDS">NMDS</option>
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23 <option value="MDS">MDS</option>
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24 <option value="PCoA">PCoA</option>
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25 </param>
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26 <param name="distance" type="select" label="Distance method" help="Utilized only if a distance matrix is required by the Ordination method selected above">
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27 <option value="bray" selected="true">bray</option>
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28 <option value="canberra">canberra</option>
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29 <option value="euclidean">euclidean</option>
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30 <option value="gower">gower</option>
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31 <option value="horn">horn</option>
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32 <option value="jaccard">jaccard</option>
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33 <option value="kulczynski">kulczynski</option>
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34 <option value="manhattan">manhattan</option>
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35 <option value="maximum">maximum</option>
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36 <option value="minkowski">minkowski</option>
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37 <option value="morisita">morisita</option>
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38 <option value="mountford">mountford</option>
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39 </param>
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40 <param name="type" type="select" label="Plot type">
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41 <option value="biplot" selected="true">biplot</option>
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42 <option value="samples">samples</option>
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43 <option value="scree">scree</option>
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44 <option value="species">species</option>
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45 <option value="split">split</option>
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46 </param>
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47 </inputs>
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48 <expand macro="outputs"/>
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49 <tests>
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50 <test>
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51 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
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52 <output name="output" ftype="pdf">
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53 <assert_contents>
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54 <has_text text="%PDF"/>
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55 <has_text text="%%EOF"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help>
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61 **What it does**
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62
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63 Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table,
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64 and generates an ordination plot of the samples.
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65
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66 **Options**
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67
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68 **Ordination method**
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69
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70 * **DCA** - Performs detrended correspondence analysis using decorana.
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71 * **CCA** - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca.
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72 * **RDA** - Performs redundancy analysis, or optionally principal components analysis, via vegan rda.
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73 * **CAP** - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale.
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74 * **NMDS** - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k).
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75 * **MDS/PCoA** - Performs principal coordinate analysis (also called principle coordinate decomposition, multidimensional scaling (MDS), or classical scaling) of a distance matrix including two correction methods for negative eigenvalues.
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76
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77 **Distance method** - Utilized only if a distance matrix is required by the Ordination method documented above.
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78
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79 **Plot type**
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80
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81 * **biplot** - Produces a combined plot with both taxa and samples.
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82 * **samples** - Produces a single plot of just the samples of the ordination.
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83 * **scree** - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis.
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84 * **species** - Produces a single plot of just the species of the ordination.
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85 * **split** - Produces a plot with both taxa and samples separated in two facet panels respectively.
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86 </help>
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87 <expand macro="citations"/>
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88 </tool>
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89