Mercurial > repos > q2d2 > qiime2__diversity__core_metrics_phylogenetic

comparison qiime2__diversity__core_metrics_phylogenetic.xml @ 3:76e136962089 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 20:57:05 +0000
parents 9d29f6a334e5
children d14296c8a1b8
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2:9d29f6a334e5 3:76e136962089
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 core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 diversity core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Core diversity metrics (phylogenetic and non-phylogenetic)</description> 14 <description>Core diversity metrics (phylogenetic and non-phylogenetic)</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 core_metrics_phylogenetic '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run diversity core_metrics_phylogenetic '$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]" help="[required] The feature table containing the samples over which diversity metrics should be computed."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples over which diversity metrics 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[Frequency]"/> 26 <filter type="add_value" value="FeatureTable[Frequency]"/>
48 </when> 48 </when>
49 </conditional> 49 </conditional>
50 </repeat> 50 </repeat>
51 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 51 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
52 <param name="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No] Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/> 52 <param name="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No] Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/>
53 <conditional name="__q2galaxy__GUI__conditional__n_jobs_or_threads__"> 53 <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] If set to `True` samples and features without metadata are included by setting all metadata values to: &quot;This element has no metadata&quot;. By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element."/>
54 <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs_or_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created for each identified CPU core on the host.">
55 <option value="auto">auto (Str)</option>
56 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
57 </param>
58 <when value="auto">
59 <param name="n_jobs_or_threads" type="hidden" value="auto"/>
60 </when>
61 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
62 <param name="n_jobs_or_threads" type="integer" min="1" value="1" label="n_jobs_or_threads: Int % Range(1, None)" help="[default: 1] [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created for each identified CPU core on the host."/>
63 </when>
64 </conditional>
65 </section> 54 </section>
66 </inputs> 55 </inputs>
67 <outputs> 56 <outputs>
68 <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/> 57 <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/>
69 <data name="faith_pd_vector" format="qza" label="${tool.name} on ${on_string}: faith_pd_vector.qza" from_work_dir="faith_pd_vector.qza"/> 58 <data name="faith_pd_vector" format="qza" label="${tool.name} on ${on_string}: faith_pd_vector.qza" from_work_dir="faith_pd_vector.qza"/>