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