# HG changeset patch
# User q2d2
# Date 1661803848 0
# Node ID 55fd8d76600647807248b9f6d606f68b1ccecd4f

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

diff -r 000000000000 -r 55fd8d766006 qiime2__longitudinal__volatility.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__longitudinal__volatility.xml	Mon Aug 29 20:10:48 2022 +0000
@@ -0,0 +1,135 @@
+<?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 volatility" id="qiime2__longitudinal__volatility" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Generate interactive volatility plot</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 volatility '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <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 column containing state (time) variable information.">
+            <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">
+            <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional]  Feature table containing metrics.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
+            </param>
+            <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>
+            <conditional name="__q2galaxy__GUI__conditional__default_group_column__" label="default_group_column: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="default_group_column: Str" help="[optional]  The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).">
+                    <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="default_group_column" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="default_group_column" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__default_metric__" label="default_metric: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="default_metric: Str" help="[optional]  Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).">
+                    <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="default_metric" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="default_metric" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param name="yscale" type="select" label="yscale: Str % Choices('linear', 'pow', 'sqrt', 'log')" display="radio">
+                <option value="linear" selected="true">linear</option>
+                <option value="pow">pow</option>
+                <option value="sqrt">sqrt</option>
+                <option value="log">log</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: longitudinal volatility
+================================
+Generate interactive volatility plot
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Generate an interactive control chart depicting the longitudinal volatility of sample metadata and/or feature frequencies across time (as set using the "state_column" parameter). Any numeric metadata column (and metadata-transformable artifacts, e.g., alpha diversity results) can be plotted on the y-axis, and are selectable using the "metric_column" selector. Metric values are averaged to compare across any categorical metadata column using the "group_column" selector. Longitudinal volatility for individual subjects sampled over time is co-plotted as "spaghetti" plots if the "individual_id_column" parameter is used. 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 55fd8d766006 test-data/.gitkeep