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annotate qiime2__diversity__core_metrics.xml @ 2:9602903a0fbd draft

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author q2d2
date Thu, 08 Jun 2023 19:37:05 +0000
parents 4b8cdacb02f5
children c18b62c7d0f8
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 diversity core-metrics" id="qiime2__diversity__core_metrics" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Core diversity metrics (non-phylogenetic)</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version diversity</version_command>
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19 <command detect_errors="exit_code">q2galaxy run diversity core_metrics '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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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.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Frequency]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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29 </param>
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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."/>
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31 <repeat name="metadata" min="1" help="[required] The sample metadata to use in the emperor plots." title="metadata: Metadata">
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32 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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33 <param name="type" type="select" label="metadata: Metadata">
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34 <option value="tsv" selected="true">Metadata from TSV</option>
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35 <option value="qza">Metadata from Artifact</option>
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36 </param>
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37 <when value="tsv">
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38 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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39 </when>
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40 <when value="qza">
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41 <param name="source" type="data" format="qza" label="Metadata Source"/>
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42 </when>
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43 </conditional>
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44 </repeat>
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45 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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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."/>
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47 <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
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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.">
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49 <option value="auto">auto (Str)</option>
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50 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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51 </param>
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52 <when value="auto">
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53 <param name="n_jobs" type="hidden" value="auto"/>
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54 </when>
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55 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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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."/>
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57 </when>
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58 </conditional>
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59 </section>
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60 </inputs>
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61 <outputs>
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62 <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/>
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63 <data name="observed_features_vector" format="qza" label="${tool.name} on ${on_string}: observed_features_vector.qza" from_work_dir="observed_features_vector.qza"/>
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64 <data name="shannon_vector" format="qza" label="${tool.name} on ${on_string}: shannon_vector.qza" from_work_dir="shannon_vector.qza"/>
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65 <data name="evenness_vector" format="qza" label="${tool.name} on ${on_string}: evenness_vector.qza" from_work_dir="evenness_vector.qza"/>
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66 <data name="jaccard_distance_matrix" format="qza" label="${tool.name} on ${on_string}: jaccard_distance_matrix.qza" from_work_dir="jaccard_distance_matrix.qza"/>
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67 <data name="bray_curtis_distance_matrix" format="qza" label="${tool.name} on ${on_string}: bray_curtis_distance_matrix.qza" from_work_dir="bray_curtis_distance_matrix.qza"/>
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68 <data name="jaccard_pcoa_results" format="qza" label="${tool.name} on ${on_string}: jaccard_pcoa_results.qza" from_work_dir="jaccard_pcoa_results.qza"/>
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69 <data name="bray_curtis_pcoa_results" format="qza" label="${tool.name} on ${on_string}: bray_curtis_pcoa_results.qza" from_work_dir="bray_curtis_pcoa_results.qza"/>
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70 <data name="jaccard_emperor" format="qzv" label="${tool.name} on ${on_string}: jaccard_emperor.qzv" from_work_dir="jaccard_emperor.qzv"/>
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71 <data name="bray_curtis_emperor" format="qzv" label="${tool.name} on ${on_string}: bray_curtis_emperor.qzv" from_work_dir="bray_curtis_emperor.qzv"/>
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72 </outputs>
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73 <tests/>
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74 <help>
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75 QIIME 2: diversity core-metrics
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76 ===============================
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77 Core diversity metrics (non-phylogenetic)
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78
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79
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80 Outputs:
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81 --------
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82 :rarefied_table.qza: The resulting rarefied feature table.
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83 :observed_features_vector.qza: Vector of Observed Features values by sample.
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84 :shannon_vector.qza: Vector of Shannon diversity values by sample.
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85 :evenness_vector.qza: Vector of Pielou's evenness values by sample.
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86 :jaccard_distance_matrix.qza: Matrix of Jaccard distances between pairs of samples.
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87 :bray_curtis_distance_matrix.qza: Matrix of Bray-Curtis distances between pairs of samples.
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88 :jaccard_pcoa_results.qza: PCoA matrix computed from Jaccard distances between samples.
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89 :bray_curtis_pcoa_results.qza: PCoA matrix computed from Bray-Curtis distances between samples.
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90 :jaccard_emperor.qzv: Emperor plot of the PCoA matrix computed from Jaccard.
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91 :bray_curtis_emperor.qzv: Emperor plot of the PCoA matrix computed from Bray-Curtis.
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92
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93 |
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94
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95 Description:
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96 ------------
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97 Applies a collection of diversity metrics (non-phylogenetic) to a feature table.
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98
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99
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100 |
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101
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102 </help>
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103 <citations>
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104 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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105 </citations>
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106 </tool>