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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:48:47 +0000
parents bea0cdf2d9c8
children 085340f69dfe
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4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2022.11.1) 9 q2galaxy (version: 2023.5.0)
10 for: 10 for:
11 qiime2 (version: 2022.11.1) 11 qiime2 (version: 2023.5.1)
12 --> 12 -->
13 <tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
14 <description>Generate interactive volatility plot</description> 14 <description>Generate interactive volatility plot</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.11</container> 16 <container type="docker">quay.io/qiime2/core:2023.5</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version longitudinal</version_command> 18 <version_command>q2galaxy version longitudinal</version_command>
19 <command detect_errors="exit_code">q2galaxy run longitudinal volatility '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run longitudinal volatility '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
105 </section> 105 </section>
106 </inputs> 106 </inputs>
107 <outputs> 107 <outputs>
108 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 108 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
109 </outputs> 109 </outputs>
110 <tests/> 110 <tests>
111 <test>
112 <repeat name="metadata">
113 <conditional name="__q2galaxy__GUI__conditional__metadata__">
114 <param name="type" value="tsv"/>
115 <param name="source" value="volatility.test0.metadata.tsv" ftype="qiime2.tabular"/>
116 </conditional>
117 </repeat>
118 <param name="state_column" value="month"/>
119 <output name="visualization" ftype="qzv">
120 <assert_contents>
121 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/data\/index.html">
122 <has_line_matching expression="^\s*&quot;month&quot;: null,$"/>
123 </has_archive_member>
124 </assert_contents>
125 </output>
126 </test>
127 </tests>
111 <help> 128 <help>
112 QIIME 2: longitudinal volatility 129 QIIME 2: longitudinal volatility
113 ================================ 130 ================================
114 Generate interactive volatility plot 131 Generate interactive volatility plot
115 132
122 139
123 Description: 140 Description:
124 ------------ 141 ------------
125 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. 142 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.
126 143
144 Examples:
145 ---------
146
147 longitudinal_volatility
148 ***********************
149 Using the ``qiime2 longitudinal volatility`` tool:
150 #. For *"metadata"*:
151
152 - Perform the following steps.
153
154 #. Leave as ``Metadata from TSV``
155 #. Set *"Metadata Source"* to ``metadata.tsv``
156
157
158 #. Set *"state_column"* to ``month``
159 #. Press the ``Execute`` button.
160
161 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
162 (Renaming is optional, but it will make any subsequent steps easier to complete.)
163
164 .. list-table::
165 :align: left
166 :header-rows: 1
167
168 * - History Name
169 - *"Name"* to set (be sure to press ``Save``)
170 * - ``#: qiime2 longitudinal volatility [...] : visualization.qzv``
171 - ``volatility-plot.qzv``
172
127 173
128 | 174 |
129 175
130 </help> 176 </help>
131 <citations> 177 <citations>