Mercurial > repos > q2d2 > qiime2__diversity__core_metrics
comparison qiime2__diversity__core_metrics.xml @ 0:c841290b1a15 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:35:49 +0000 |
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children | 4b8cdacb02f5 |
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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 core-metrics" id="qiime2__diversity__core_metrics" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Core diversity metrics (non-phylogenetic)</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 core_metrics '$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]" help="[required] The feature table containing the samples over which diversity metrics should be computed."> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="FeatureTable[Frequency]"/> | |
27 </options> | |
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> | |
29 </param> | |
30 <param name="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required] The total frequency that each sample should be rarefied to prior to computing diversity metrics."/> | |
31 <repeat name="metadata" min="1" help="[required] The sample metadata to use in the emperor plots." title="metadata: Metadata"> | |
32 <conditional name="__q2galaxy__GUI__conditional__metadata__"> | |
33 <param name="type" type="select" label="metadata: Metadata"> | |
34 <option value="tsv" selected="true">Metadata from TSV</option> | |
35 <option value="qza">Metadata from Artifact</option> | |
36 </param> | |
37 <when value="tsv"> | |
38 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> | |
39 </when> | |
40 <when value="qza"> | |
41 <param name="source" type="data" format="qza" label="Metadata Source"/> | |
42 </when> | |
43 </conditional> | |
44 </repeat> | |
45 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
46 <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."/> | |
47 <conditional name="__q2galaxy__GUI__conditional__n_jobs__"> | |
48 <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] [beta methods only] - 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."> | |
49 <option value="auto">auto (Str)</option> | |
50 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> | |
51 </param> | |
52 <when value="auto"> | |
53 <param name="n_jobs" type="hidden" value="auto"/> | |
54 </when> | |
55 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> | |
56 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] [beta methods only] - 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."/> | |
57 </when> | |
58 </conditional> | |
59 </section> | |
60 </inputs> | |
61 <outputs> | |
62 <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/> | |
63 <data name="observed_features_vector" format="qza" label="${tool.name} on ${on_string}: observed_features_vector.qza" from_work_dir="observed_features_vector.qza"/> | |
64 <data name="shannon_vector" format="qza" label="${tool.name} on ${on_string}: shannon_vector.qza" from_work_dir="shannon_vector.qza"/> | |
65 <data name="evenness_vector" format="qza" label="${tool.name} on ${on_string}: evenness_vector.qza" from_work_dir="evenness_vector.qza"/> | |
66 <data name="jaccard_distance_matrix" format="qza" label="${tool.name} on ${on_string}: jaccard_distance_matrix.qza" from_work_dir="jaccard_distance_matrix.qza"/> | |
67 <data name="bray_curtis_distance_matrix" format="qza" label="${tool.name} on ${on_string}: bray_curtis_distance_matrix.qza" from_work_dir="bray_curtis_distance_matrix.qza"/> | |
68 <data name="jaccard_pcoa_results" format="qza" label="${tool.name} on ${on_string}: jaccard_pcoa_results.qza" from_work_dir="jaccard_pcoa_results.qza"/> | |
69 <data name="bray_curtis_pcoa_results" format="qza" label="${tool.name} on ${on_string}: bray_curtis_pcoa_results.qza" from_work_dir="bray_curtis_pcoa_results.qza"/> | |
70 <data name="jaccard_emperor" format="qzv" label="${tool.name} on ${on_string}: jaccard_emperor.qzv" from_work_dir="jaccard_emperor.qzv"/> | |
71 <data name="bray_curtis_emperor" format="qzv" label="${tool.name} on ${on_string}: bray_curtis_emperor.qzv" from_work_dir="bray_curtis_emperor.qzv"/> | |
72 </outputs> | |
73 <tests/> | |
74 <help> | |
75 QIIME 2: diversity core-metrics | |
76 =============================== | |
77 Core diversity metrics (non-phylogenetic) | |
78 | |
79 | |
80 Outputs: | |
81 -------- | |
82 :rarefied_table.qza: The resulting rarefied feature table. | |
83 :observed_features_vector.qza: Vector of Observed Features values by sample. | |
84 :shannon_vector.qza: Vector of Shannon diversity values by sample. | |
85 :evenness_vector.qza: Vector of Pielou's evenness values by sample. | |
86 :jaccard_distance_matrix.qza: Matrix of Jaccard distances between pairs of samples. | |
87 :bray_curtis_distance_matrix.qza: Matrix of Bray-Curtis distances between pairs of samples. | |
88 :jaccard_pcoa_results.qza: PCoA matrix computed from Jaccard distances between samples. | |
89 :bray_curtis_pcoa_results.qza: PCoA matrix computed from Bray-Curtis distances between samples. | |
90 :jaccard_emperor.qzv: Emperor plot of the PCoA matrix computed from Jaccard. | |
91 :bray_curtis_emperor.qzv: Emperor plot of the PCoA matrix computed from Bray-Curtis. | |
92 | |
93 | | |
94 | |
95 Description: | |
96 ------------ | |
97 Applies a collection of diversity metrics (non-phylogenetic) to a feature table. | |
98 | |
99 | |
100 | | |
101 | |
102 </help> | |
103 <citations> | |
104 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
105 </citations> | |
106 </tool> |