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annotate qiime2__longitudinal__feature_volatility.xml @ 0:89d35e7b6d90 draft

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author q2d2
date Mon, 29 Aug 2022 20:12:21 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2022, QIIME 2 development team.
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4
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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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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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">
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14 <description>Feature volatility analysis</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</container>
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17 </requirements>
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18 <version_command>q2galaxy version longitudinal</version_command>
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19 <command detect_errors="aggressive">q2galaxy run longitudinal feature_volatility '$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] Feature table containing all features that should be used for target prediction.">
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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 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
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31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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32 <param name="type" type="select" label="metadata: Metadata">
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33 <option value="tsv" selected="true">Metadata from TSV</option>
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34 <option value="qza">Metadata from Artifact</option>
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35 </param>
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36 <when value="tsv">
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37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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38 </when>
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39 <when value="qza">
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40 <param name="source" type="data" format="qza" label="Metadata Source"/>
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41 </when>
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42 </conditional>
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43 </repeat>
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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.">
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45 <sanitizer>
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46 <valid initial="string.printable"/>
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47 </sanitizer>
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48 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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49 </param>
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50 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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51 <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">
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52 <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional] Metadata column containing IDs for individual subjects.">
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53 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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54 <option value="__q2galaxy__::control::provide">Provide a value</option>
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55 </param>
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56 <when value="__q2galaxy__::control::default">
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57 <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>
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58 </when>
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59 <when value="__q2galaxy__::control::provide">
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60 <param name="individual_id_column" type="text">
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61 <sanitizer>
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62 <valid initial="string.printable"/>
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63 </sanitizer>
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64 </param>
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65 </when>
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66 </conditional>
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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."/>
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68 <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional] Seed used by random number generator."/>
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69 <param name="n_jobs" type="integer" value="1" label="n_jobs: Int" help="[default: 1] Number of jobs to run in parallel."/>
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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."/>
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71 <param name="estimator" type="select" label="estimator: Str % Choices('RandomForestRegressor', 'ExtraTreesRegressor', 'GradientBoostingRegressor', 'AdaBoostRegressor', 'ElasticNet', 'Ridge', 'Lasso', 'KNeighborsRegressor', 'LinearSVR', 'SVR')">
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72 <option value="RandomForestRegressor" selected="true">RandomForestRegressor</option>
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73 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
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74 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
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75 <option value="AdaBoostRegressor">AdaBoostRegressor</option>
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76 <option value="ElasticNet">ElasticNet</option>
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77 <option value="Ridge">Ridge</option>
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78 <option value="Lasso">Lasso</option>
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79 <option value="KNeighborsRegressor">KNeighborsRegressor</option>
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80 <option value="LinearSVR">LinearSVR</option>
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81 <option value="SVR">SVR</option>
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82 </param>
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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."/>
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84 <param name="missing_samples" type="select" label="missing_samples: Str % Choices('error', 'ignore')" display="radio">
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85 <option value="error" selected="true">error</option>
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86 <option value="ignore">ignore</option>
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87 </param>
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88 <conditional name="__q2galaxy__GUI__conditional__importance_threshold__">
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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.">
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90 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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91 <option value="q1">q1 (Str)</option>
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92 <option value="q2">q2 (Str)</option>
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93 <option value="q3">q3 (Str)</option>
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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>
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95 </param>
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96 <when value="__q2galaxy__::literal::None">
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97 <param name="importance_threshold" type="hidden" value="__q2galaxy__::literal::None"/>
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98 </when>
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99 <when value="q1">
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100 <param name="importance_threshold" type="hidden" value="q1"/>
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101 </when>
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102 <when value="q2">
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103 <param name="importance_threshold" type="hidden" value="q2"/>
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104 </when>
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105 <when value="q3">
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106 <param name="importance_threshold" type="hidden" value="q3"/>
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107 </when>
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108 <when value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)">
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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."/>
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110 </when>
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111 </conditional>
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112 <conditional name="__q2galaxy__GUI__conditional__feature_count__">
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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.">
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114 <option value="all">all (Str)</option>
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115 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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116 </param>
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117 <when value="all">
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118 <param name="feature_count" type="hidden" value="all"/>
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119 </when>
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120 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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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."/>
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122 </when>
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123 </conditional>
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124 </section>
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125 </inputs>
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126 <outputs>
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127 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
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128 <data name="feature_importance" format="qza" label="${tool.name} on ${on_string}: feature_importance.qza" from_work_dir="feature_importance.qza"/>
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129 <data name="volatility_plot" format="qzv" label="${tool.name} on ${on_string}: volatility_plot.qzv" from_work_dir="volatility_plot.qzv"/>
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130 <data name="accuracy_results" format="qzv" label="${tool.name} on ${on_string}: accuracy_results.qzv" from_work_dir="accuracy_results.qzv"/>
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131 <data name="sample_estimator" format="qza" label="${tool.name} on ${on_string}: sample_estimator.qza" from_work_dir="sample_estimator.qza"/>
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132 </outputs>
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133 <tests/>
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134 <help>
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135 QIIME 2: longitudinal feature-volatility
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136 ========================================
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137 Feature volatility analysis
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138
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139
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140 Outputs:
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141 --------
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142 :filtered_table.qza: Feature table containing only important features.
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143 :feature_importance.qza: Importance of each input feature to model accuracy.
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144 :volatility_plot.qzv: Interactive volatility plot visualization.
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145 :accuracy_results.qzv: Accuracy results visualization.
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146 :sample_estimator.qza: Trained sample regressor.
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147
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148 |
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149
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150 Description:
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151 ------------
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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.
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154
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155 |
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156
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157 </help>
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158 <citations>
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159 <citation type="doi">10.1128/mSystems.00219-18</citation>
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160 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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161 </citations>
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162 </tool>