Mercurial > repos > q2d2 > qiime2__diversity__mantel

comparison qiime2__diversity__mantel.xml @ 0:5f235e10be72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:37:54 +0000
parents
children f5f2c923cda4
comparison
equal deleted inserted replaced
-1:000000000000 0:5f235e10be72
1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 diversity mantel" id="qiime2__diversity__mantel" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Apply the Mantel test to two distance matrices</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version diversity</version_command>
19 <command detect_errors="aggressive">q2galaxy run diversity mantel '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="dm1" type="data" format="qza" label="dm1: DistanceMatrix" help="[required] Matrix of distances between pairs of samples.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="DistanceMatrix"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
29 </param>
30 <param name="dm2" type="data" format="qza" label="dm2: DistanceMatrix" help="[required] Matrix of distances between pairs of samples.">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="DistanceMatrix"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
35 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
37 <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio">
38 <option value="spearman" selected="true">spearman</option>
39 <option value="pearson">pearson</option>
40 </param>
41 <param name="permutations" type="integer" min="0" value="999" label="permutations: Int % Range(0, None)" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
42 <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No] If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs."/>
43 <param name="label1" type="text" value="Distance Matrix 1" label="label1: Str" help="[default: 'Distance Matrix 1'] Label for `dm1` in the output visualization.">
44 <sanitizer>
45 <valid initial="string.printable"/>
46 </sanitizer>
47 </param>
48 <param name="label2" type="text" value="Distance Matrix 2" label="label2: Str" help="[default: 'Distance Matrix 2'] Label for `dm2` in the output visualization.">
49 <sanitizer>
50 <valid initial="string.printable"/>
51 </sanitizer>
52 </param>
53 </section>
54 </inputs>
55 <outputs>
56 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
57 </outputs>
58 <tests/>
59 <help>
60 QIIME 2: diversity mantel
61 =========================
62 Apply the Mantel test to two distance matrices
63
64
65 Outputs:
66 --------
67 :visualization.qzv: &lt;no description&gt;
68
69 |
70
71 Description:
72 ------------
73 Apply a two-sided Mantel test to identify correlation between two distance matrices.
74
75 Note: the directionality of the comparison has no bearing on the results. Thus, comparing distance matrix X to distance matrix Y is equivalent to comparing Y to X.
76
77 Note: the order of samples within the two distance matrices does not need to be the same; the distance matrices will be reordered before applying the Mantel test.
78
79 See the scikit-bio docs for more details about the Mantel test:
80
81 http://scikit-bio.org/docs/latest/generated/skbio.stats.distance.mantel
82
83
84 |
85
86 </help>
87 <citations>
88 <citation type="bibtex">@article{cite1,
89 author = {Mantel, Nathan},
90 journal = {Cancer research},
91 number = {2 Part 1},
92 pages = {209--220},
93 publisher = {AACR},
94 title = {The detection of disease clustering and a generalized regression approach},
95 volume = {27},
96 year = {1967}
97 }
98 </citation>
99 <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>
100 <citation type="doi">https://doi.org/10.2307/1422689</citation>
101 <citation type="doi">10.1038/s41587-019-0209-9</citation>
102 </citations>
103 </tool>