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comparison qiime2__diversity__beta.xml @ 3:525d07dd31b2 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 20:56:59 +0000
parents f5026cf3e156
children 7ed55f1323ee
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2:f5026cf3e156 3:525d07dd31b2
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <tool name="qiime2 diversity beta" id="qiime2__diversity__beta" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity beta" id="qiime2__diversity__beta" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Beta diversity</description> 14 <description>Beta diversity</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version diversity</version_command> 18 <version_command>q2galaxy version diversity</version_command>
19 <command detect_errors="exit_code">q2galaxy run diversity beta '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity beta '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 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."> 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"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> 26 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[Frequency]"/> 27 <filter type="add_value" value="FeatureTable[Frequency]"/>
28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
29 </options> 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> 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> 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')"> 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> 33 <option value="__q2galaxy__::literal::None">Selection required</option>
56 <option value="yule">yule</option> 56 <option value="yule">yule</option>
57 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> 57 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
58 </param> 58 </param>
59 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 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."/> 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> 61 </section>
74 </inputs> 62 </inputs>
75 <outputs> 63 <outputs>
76 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> 64 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
77 </outputs> 65 </outputs>