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comparison qiime2__diversity__beta.xml @ 0:b9c031cf3ea5 draft

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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 19:32:01 +0000
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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 beta" id="qiime2__diversity__beta" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Beta diversity</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 beta '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples over which beta diversity should be computed.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
31 </param>
32 <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
33 <option value="__q2galaxy__::literal::None">Selection required</option>
34 <option value="aitchison">aitchison</option>
35 <option value="braycurtis">braycurtis</option>
36 <option value="canberra">canberra</option>
37 <option value="canberra_adkins">canberra_adkins</option>
38 <option value="chebyshev">chebyshev</option>
39 <option value="cityblock">cityblock</option>
40 <option value="correlation">correlation</option>
41 <option value="cosine">cosine</option>
42 <option value="dice">dice</option>
43 <option value="euclidean">euclidean</option>
44 <option value="hamming">hamming</option>
45 <option value="jaccard">jaccard</option>
46 <option value="jensenshannon">jensenshannon</option>
47 <option value="kulsinski">kulsinski</option>
48 <option value="matching">matching</option>
49 <option value="minkowski">minkowski</option>
50 <option value="rogerstanimoto">rogerstanimoto</option>
51 <option value="russellrao">russellrao</option>
52 <option value="seuclidean">seuclidean</option>
53 <option value="sokalmichener">sokalmichener</option>
54 <option value="sokalsneath">sokalsneath</option>
55 <option value="sqeuclidean">sqeuclidean</option>
56 <option value="yule">yule</option>
57 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
58 </param>
59 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
60 <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics."/>
61 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
62 <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.">
63 <option value="auto">auto (Str)</option>
64 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
65 </param>
66 <when value="auto">
67 <param name="n_jobs" type="hidden" value="auto"/>
68 </when>
69 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
70 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
71 </when>
72 </conditional>
73 </section>
74 </inputs>
75 <outputs>
76 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
77 </outputs>
78 <tests/>
79 <help>
80 QIIME 2: diversity beta
81 =======================
82 Beta diversity
83
84
85 Outputs:
86 --------
87 :distance_matrix.qza: The resulting distance matrix.
88
89 |
90
91 Description:
92 ------------
93 Computes a user-specified beta diversity metric for all pairs of samples in a feature table.
94
95
96 |
97
98 </help>
99 <citations>
100 <citation type="doi">10.1038/s41587-019-0209-9</citation>
101 </citations>
102 </tool>