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comparison qiime2__longitudinal__volatility.xml @ 0:55fd8d766006 draft

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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 20:10:48 +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 volatility" id="qiime2__longitudinal__volatility" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Generate interactive volatility plot</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 volatility '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
25 <conditional name="__q2galaxy__GUI__conditional__metadata__">
26 <param name="type" type="select" label="metadata: Metadata">
27 <option value="tsv" selected="true">Metadata from TSV</option>
28 <option value="qza">Metadata from Artifact</option>
29 </param>
30 <when value="tsv">
31 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
32 </when>
33 <when value="qza">
34 <param name="source" type="data" format="qza" label="Metadata Source"/>
35 </when>
36 </conditional>
37 </repeat>
38 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information.">
39 <sanitizer>
40 <valid initial="string.printable"/>
41 </sanitizer>
42 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
43 </param>
44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
45 <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table containing metrics.">
46 <options options_filter_attribute="metadata.semantic_type">
47 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
48 </options>
49 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
50 </param>
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 <conditional name="__q2galaxy__GUI__conditional__default_group_column__" label="default_group_column: Str">
68 <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).">
69 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
70 <option value="__q2galaxy__::control::provide">Provide a value</option>
71 </param>
72 <when value="__q2galaxy__::control::default">
73 <param name="default_group_column" type="hidden" value="__q2galaxy__::literal::None"/>
74 </when>
75 <when value="__q2galaxy__::control::provide">
76 <param name="default_group_column" type="text">
77 <sanitizer>
78 <valid initial="string.printable"/>
79 </sanitizer>
80 </param>
81 </when>
82 </conditional>
83 <conditional name="__q2galaxy__GUI__conditional__default_metric__" label="default_metric: Str">
84 <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).">
85 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
86 <option value="__q2galaxy__::control::provide">Provide a value</option>
87 </param>
88 <when value="__q2galaxy__::control::default">
89 <param name="default_metric" type="hidden" value="__q2galaxy__::literal::None"/>
90 </when>
91 <when value="__q2galaxy__::control::provide">
92 <param name="default_metric" type="text">
93 <sanitizer>
94 <valid initial="string.printable"/>
95 </sanitizer>
96 </param>
97 </when>
98 </conditional>
99 <param name="yscale" type="select" label="yscale: Str % Choices('linear', 'pow', 'sqrt', 'log')" display="radio">
100 <option value="linear" selected="true">linear</option>
101 <option value="pow">pow</option>
102 <option value="sqrt">sqrt</option>
103 <option value="log">log</option>
104 </param>
105 </section>
106 </inputs>
107 <outputs>
108 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
109 </outputs>
110 <tests/>
111 <help>
112 QIIME 2: longitudinal volatility
113 ================================
114 Generate interactive volatility plot
115
116
117 Outputs:
118 --------
119 :visualization.qzv: &lt;no description&gt;
120
121 |
122
123 Description:
124 ------------
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.
126
127
128 |
129
130 </help>
131 <citations>
132 <citation type="doi">10.1128/mSystems.00219-18</citation>
133 <citation type="doi">10.1038/s41587-019-0209-9</citation>
134 </citations>
135 </tool>