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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:12:21 +0000
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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 longitudinal feature-volatility" id="qiime2__longitudinal__feature_volatility" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Feature volatility analysis</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version longitudinal</version_command>
19 <command detect_errors="aggressive">q2galaxy run longitudinal feature_volatility '$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] Feature table containing all features that should be used for target prediction.">
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 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
32 <param name="type" type="select" label="metadata: Metadata">
33 <option value="tsv" selected="true">Metadata from TSV</option>
34 <option value="qza">Metadata from Artifact</option>
35 </param>
36 <when value="tsv">
37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
38 </when>
39 <when value="qza">
40 <param name="source" type="data" format="qza" label="Metadata Source"/>
41 </when>
42 </conditional>
43 </repeat>
44 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata containing collection time (state) values for each sample. Must contain exclusively numeric values.">
45 <sanitizer>
46 <valid initial="string.printable"/>
47 </sanitizer>
48 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
49 </param>
50 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
51 <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">
52 <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional] Metadata column containing IDs for individual subjects.">
53 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
54 <option value="__q2galaxy__::control::provide">Provide a value</option>
55 </param>
56 <when value="__q2galaxy__::control::default">
57 <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>
58 </when>
59 <when value="__q2galaxy__::control::provide">
60 <param name="individual_id_column" type="text">
61 <sanitizer>
62 <valid initial="string.printable"/>
63 </sanitizer>
64 </param>
65 </when>
66 </conditional>
67 <param name="cv" type="integer" min="1" value="5" label="cv: Int % Range(1, None)" help="[default: 5] Number of k-fold cross-validations to perform."/>
68 <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional] Seed used by random number generator."/>
69 <param name="n_jobs" type="integer" value="1" label="n_jobs: Int" help="[default: 1] Number of jobs to run in parallel."/>
70 <param name="n_estimators" type="integer" min="1" value="100" label="n_estimators: Int % Range(1, None)" help="[default: 100] Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements. This parameter only affects ensemble estimators, such as Random Forest, AdaBoost, ExtraTrees, and GradientBoosting."/>
71 <param name="estimator" type="select" label="estimator: Str % Choices('RandomForestRegressor', 'ExtraTreesRegressor', 'GradientBoostingRegressor', 'AdaBoostRegressor', 'ElasticNet', 'Ridge', 'Lasso', 'KNeighborsRegressor', 'LinearSVR', 'SVR')">
72 <option value="RandomForestRegressor" selected="true">RandomForestRegressor</option>
73 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
74 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
75 <option value="AdaBoostRegressor">AdaBoostRegressor</option>
76 <option value="ElasticNet">ElasticNet</option>
77 <option value="Ridge">Ridge</option>
78 <option value="Lasso">Lasso</option>
79 <option value="KNeighborsRegressor">KNeighborsRegressor</option>
80 <option value="LinearSVR">LinearSVR</option>
81 <option value="SVR">SVR</option>
82 </param>
83 <param name="parameter_tuning" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parameter_tuning: Bool" help="[default: No] Automatically tune hyperparameters using random grid search."/>
84 <param name="missing_samples" type="select" label="missing_samples: Str % Choices('error', 'ignore')" display="radio">
85 <option value="error" selected="true">error</option>
86 <option value="ignore">ignore</option>
87 </param>
88 <conditional name="__q2galaxy__GUI__conditional__importance_threshold__">
89 <param name="__q2galaxy__GUI__select__" type="select" label="importance_threshold: Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3')" help="[optional] Filter feature table to exclude any features with an importance score less than this threshold. Set to &quot;q1&quot;, &quot;q2&quot;, or &quot;q3&quot; to select the first, second, or third quartile of values. Set to &quot;None&quot; to disable this filter.">
90 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
91 <option value="q1">q1 (Str)</option>
92 <option value="q2">q2 (Str)</option>
93 <option value="q3">q3 (Str)</option>
94 <option value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)">Provide a value (Float % Range(0, None, inclusive_start=False))</option>
95 </param>
96 <when value="__q2galaxy__::literal::None">
97 <param name="importance_threshold" type="hidden" value="__q2galaxy__::literal::None"/>
98 </when>
99 <when value="q1">
100 <param name="importance_threshold" type="hidden" value="q1"/>
101 </when>
102 <when value="q2">
103 <param name="importance_threshold" type="hidden" value="q2"/>
104 </when>
105 <when value="q3">
106 <param name="importance_threshold" type="hidden" value="q3"/>
107 </when>
108 <when value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)">
109 <param name="importance_threshold" type="float" min="1e-06" value="" label="importance_threshold: Float % Range(0, None, inclusive_start=False)" help="[required] Filter feature table to exclude any features with an importance score less than this threshold. Set to &quot;q1&quot;, &quot;q2&quot;, or &quot;q3&quot; to select the first, second, or third quartile of values. Set to &quot;None&quot; to disable this filter."/>
110 </when>
111 </conditional>
112 <conditional name="__q2galaxy__GUI__conditional__feature_count__">
113 <param name="__q2galaxy__GUI__select__" type="select" label="feature_count: Int % Range(1, None) | Str % Choices('all')" help="[default: 100] Filter feature table to include top N most important features. Set to &quot;all&quot; to include all features.">
114 <option value="all">all (Str)</option>
115 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
116 </param>
117 <when value="all">
118 <param name="feature_count" type="hidden" value="all"/>
119 </when>
120 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
121 <param name="feature_count" type="integer" min="1" value="100" label="feature_count: Int % Range(1, None)" help="[default: 100] Filter feature table to include top N most important features. Set to &quot;all&quot; to include all features."/>
122 </when>
123 </conditional>
124 </section>
125 </inputs>
126 <outputs>
127 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
128 <data name="feature_importance" format="qza" label="${tool.name} on ${on_string}: feature_importance.qza" from_work_dir="feature_importance.qza"/>
129 <data name="volatility_plot" format="qzv" label="${tool.name} on ${on_string}: volatility_plot.qzv" from_work_dir="volatility_plot.qzv"/>
130 <data name="accuracy_results" format="qzv" label="${tool.name} on ${on_string}: accuracy_results.qzv" from_work_dir="accuracy_results.qzv"/>
131 <data name="sample_estimator" format="qza" label="${tool.name} on ${on_string}: sample_estimator.qza" from_work_dir="sample_estimator.qza"/>
132 </outputs>
133 <tests/>
134 <help>
135 QIIME 2: longitudinal feature-volatility
136 ========================================
137 Feature volatility analysis
138
139
140 Outputs:
141 --------
142 :filtered_table.qza: Feature table containing only important features.
143 :feature_importance.qza: Importance of each input feature to model accuracy.
144 :volatility_plot.qzv: Interactive volatility plot visualization.
145 :accuracy_results.qzv: Accuracy results visualization.
146 :sample_estimator.qza: Trained sample regressor.
147
148 |
149
150 Description:
151 ------------
152 Identify features that are predictive of a numeric metadata column, state_column (e.g., time), and plot their relative frequencies across states using interactive feature volatility plots. A supervised learning regressor is used to identify important features and assess their ability to predict sample states. state_column will typically be a measure of time, but any numeric metadata column can be used.
153
154
155 |
156
157 </help>
158 <citations>
159 <citation type="doi">10.1128/mSystems.00219-18</citation>
160 <citation type="doi">10.1038/s41587-019-0209-9</citation>
161 </citations>
162 </tool>