Mercurial > repos > iuc > phyloseq_plot_ordination

annotate phyloseq_plot_ordination.xml @ 2:dfe800a3faaf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author iuc
date Sat, 16 Mar 2024 07:56:05 +0000
parents 92e77800ef2c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
1 <tool id="phyloseq_plot_ordination" name="Phyloseq: plot ordination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
2 <description></description>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
3 <macros>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
5 </macros>
1
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
iuc
parents: 0
diff changeset
6 <expand macro="bio_tools"/>
0
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
9 Rscript '${__tool_directory__}/phyloseq_plot_ordination.R'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
10 --input '$input'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
11 --method '$method'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
12 --distance '$distance'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
13 --type '$type'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
14 --output '$output'
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
15 ]]></command>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
16 <inputs>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
17 <expand macro="phyloseq_input"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
18 <param name="method" type="select" label="Ordination method">
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
19 <option value="DCA" selected="true">DCA</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
20 <option value="CCA">CCA</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
21 <option value="RDA">RDA</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
22 <option value="CAP">CAP</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
23 <option value="NMDS">NMDS</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
24 <option value="MDS">MDS</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
25 <option value="PCoA">PCoA</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
26 </param>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
27 <param name="distance" type="select" label="Distance method" help="Utilized only if a distance matrix is required by the Ordination method selected above">
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
28 <option value="bray" selected="true">bray</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
29 <option value="canberra">canberra</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
30 <option value="euclidean">euclidean</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
31 <option value="gower">gower</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
32 <option value="horn">horn</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
33 <option value="jaccard">jaccard</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
34 <option value="kulczynski">kulczynski</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
35 <option value="manhattan">manhattan</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
36 <option value="maximum">maximum</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
37 <option value="minkowski">minkowski</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
38 <option value="morisita">morisita</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
39 <option value="mountford">mountford</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
40 </param>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
41 <param name="type" type="select" label="Plot type">
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
42 <option value="biplot" selected="true">biplot</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
43 <option value="samples">samples</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
44 <option value="scree">scree</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
45 <option value="species">species</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
46 <option value="split">split</option>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
47 </param>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
48 </inputs>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
49 <expand macro="outputs"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
50 <tests>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
51 <test>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
52 <param name="input" value="output.phyloseq" ftype="phyloseq"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
53 <output name="output" ftype="pdf">
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
54 <assert_contents>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
55 <has_text text="%PDF"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
56 <has_text text="%%EOF"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
57 </assert_contents>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
58 </output>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
59 </test>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
60 </tests>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
61 <help>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
62 **What it does**
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
63
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
64 Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table,
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
65 and generates an ordination plot of the samples.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
66
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
67 **Options**
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
68
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
69 **Ordination method**
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
70
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
71 * **DCA** - Performs detrended correspondence analysis using decorana.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
72 * **CCA** - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
73 * **RDA** - Performs redundancy analysis, or optionally principal components analysis, via vegan rda.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
74 * **CAP** - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
75 * **NMDS** - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k).
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
76 * **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.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
77
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
78 **Distance method** - Utilized only if a distance matrix is required by the Ordination method documented above.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
79
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
80 **Plot type**
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
81
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
82 * **biplot** - Produces a combined plot with both taxa and samples.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
83 * **samples** - Produces a single plot of just the samples of the ordination.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
84 * **scree** - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
85 * **species** - Produces a single plot of just the species of the ordination.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
86 * **split** - Produces a plot with both taxa and samples separated in two facet panels respectively.
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
87 </help>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
88 <expand macro="citations"/>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
89 </tool>
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff changeset
90