# HG changeset patch
# User q2d2
# Date 1661803941 0
# Node ID 89d35e7b6d90ca04eefa040fb2ee85bbc64c814a

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 89d35e7b6d90 qiime2__longitudinal__feature_volatility.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__longitudinal__feature_volatility.xml	Mon Aug 29 20:12:21 2022 +0000
@@ -0,0 +1,162 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, QIIME 2 development team.
+
+Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
+-->
+<!--
+This tool was automatically generated by:
+    q2galaxy (version: 2022.8.1)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<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">
+    <description>Feature volatility analysis</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version longitudinal</version_command>
+    <command detect_errors="aggressive">q2galaxy run longitudinal feature_volatility '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <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.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <repeat name="metadata" min="1" help="[required]  Sample metadata file containing individual_id_column." title="metadata: Metadata">
+            <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                <param name="type" type="select" label="metadata: Metadata">
+                    <option value="tsv" selected="true">Metadata from TSV</option>
+                    <option value="qza">Metadata from Artifact</option>
+                </param>
+                <when value="tsv">
+                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                </when>
+            </conditional>
+        </repeat>
+        <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.">
+            <sanitizer>
+                <valid initial="string.printable"/>
+            </sanitizer>
+            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional]  Metadata column containing IDs for individual subjects.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="individual_id_column" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <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."/>
+            <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional]  Seed used by random number generator."/>
+            <param name="n_jobs" type="integer" value="1" label="n_jobs: Int" help="[default: 1]  Number of jobs to run in parallel."/>
+            <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."/>
+            <param name="estimator" type="select" label="estimator: Str % Choices('RandomForestRegressor', 'ExtraTreesRegressor', 'GradientBoostingRegressor', 'AdaBoostRegressor', 'ElasticNet', 'Ridge', 'Lasso', 'KNeighborsRegressor', 'LinearSVR', 'SVR')">
+                <option value="RandomForestRegressor" selected="true">RandomForestRegressor</option>
+                <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
+                <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
+                <option value="AdaBoostRegressor">AdaBoostRegressor</option>
+                <option value="ElasticNet">ElasticNet</option>
+                <option value="Ridge">Ridge</option>
+                <option value="Lasso">Lasso</option>
+                <option value="KNeighborsRegressor">KNeighborsRegressor</option>
+                <option value="LinearSVR">LinearSVR</option>
+                <option value="SVR">SVR</option>
+            </param>
+            <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."/>
+            <param name="missing_samples" type="select" label="missing_samples: Str % Choices('error', 'ignore')" display="radio">
+                <option value="error" selected="true">error</option>
+                <option value="ignore">ignore</option>
+            </param>
+            <conditional name="__q2galaxy__GUI__conditional__importance_threshold__">
+                <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.">
+                    <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                    <option value="q1">q1 (Str)</option>
+                    <option value="q2">q2 (Str)</option>
+                    <option value="q3">q3 (Str)</option>
+                    <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>
+                </param>
+                <when value="__q2galaxy__::literal::None">
+                    <param name="importance_threshold" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="q1">
+                    <param name="importance_threshold" type="hidden" value="q1"/>
+                </when>
+                <when value="q2">
+                    <param name="importance_threshold" type="hidden" value="q2"/>
+                </when>
+                <when value="q3">
+                    <param name="importance_threshold" type="hidden" value="q3"/>
+                </when>
+                <when value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)">
+                    <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."/>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__feature_count__">
+                <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.">
+                    <option value="all">all (Str)</option>
+                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
+                </param>
+                <when value="all">
+                    <param name="feature_count" type="hidden" value="all"/>
+                </when>
+                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
+                    <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."/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
+        <data name="feature_importance" format="qza" label="${tool.name} on ${on_string}: feature_importance.qza" from_work_dir="feature_importance.qza"/>
+        <data name="volatility_plot" format="qzv" label="${tool.name} on ${on_string}: volatility_plot.qzv" from_work_dir="volatility_plot.qzv"/>
+        <data name="accuracy_results" format="qzv" label="${tool.name} on ${on_string}: accuracy_results.qzv" from_work_dir="accuracy_results.qzv"/>
+        <data name="sample_estimator" format="qza" label="${tool.name} on ${on_string}: sample_estimator.qza" from_work_dir="sample_estimator.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: longitudinal feature-volatility
+========================================
+Feature volatility analysis
+
+
+Outputs:
+--------
+:filtered_table.qza: Feature table containing only important features.
+:feature_importance.qza: Importance of each input feature to model accuracy.
+:volatility_plot.qzv: Interactive volatility plot visualization.
+:accuracy_results.qzv: Accuracy results visualization.
+:sample_estimator.qza: Trained sample regressor.
+
+|  
+
+Description:
+------------
+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.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1128/mSystems.00219-18</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 89d35e7b6d90 test-data/.gitkeep