Mercurial > repos > q2d2 > qiime2__diversity__beta

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:38:25 +0000
parents 7ed55f1323ee
children
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 diversity beta" id="qiime2__diversity__beta" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Beta diversity</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version diversity</version_command>
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22 <command detect_errors="exit_code">q2galaxy run diversity beta '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <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.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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31 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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32 </options>
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33 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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34 </param>
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35 <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
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36 <option value="__q2galaxy__::literal::None">Selection required</option>
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37 <option value="aitchison">aitchison</option>
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38 <option value="braycurtis">braycurtis</option>
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39 <option value="canberra">canberra</option>
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40 <option value="canberra_adkins">canberra_adkins</option>
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41 <option value="chebyshev">chebyshev</option>
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42 <option value="cityblock">cityblock</option>
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43 <option value="correlation">correlation</option>
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44 <option value="cosine">cosine</option>
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45 <option value="dice">dice</option>
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46 <option value="euclidean">euclidean</option>
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47 <option value="hamming">hamming</option>
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48 <option value="jaccard">jaccard</option>
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49 <option value="jensenshannon">jensenshannon</option>
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50 <option value="matching">matching</option>
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51 <option value="minkowski">minkowski</option>
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52 <option value="rogerstanimoto">rogerstanimoto</option>
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53 <option value="russellrao">russellrao</option>
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54 <option value="seuclidean">seuclidean</option>
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55 <option value="sokalmichener">sokalmichener</option>
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56 <option value="sokalsneath">sokalsneath</option>
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57 <option value="sqeuclidean">sqeuclidean</option>
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58 <option value="yule">yule</option>
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59 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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60 </param>
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61 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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62 <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."/>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
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67 </outputs>
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68 <tests/>
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69 <help>
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70 QIIME 2: diversity beta
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71 =======================
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72 Beta diversity
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73
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74
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75 Outputs:
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76 --------
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77 :distance_matrix.qza: The resulting distance matrix.
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78
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79 |
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80
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81 Description:
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82 ------------
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83 Computes a user-specified beta diversity metric for all pairs of samples in a feature table.
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84
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85
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86 |
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87
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88 </help>
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89 <citations>
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90 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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91 </citations>
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92 </tool>