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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:50:44 +0000
parents e6978c621d70
children bc3a80afa08d
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0:e6978c621d70 1:7c9ec8b8b7f8
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2022, QIIME 2 development team. 3 Copyright (c) 2023, QIIME 2 development team.
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: 2022.8.1) 9 q2galaxy (version: 2022.11.1)
10 for: 10 for:
11 qiime2 (version: 2022.8.1) 11 qiime2 (version: 2022.11.1)
12 --> 12 -->
13 <tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 emperor plot" id="qiime2__emperor__plot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Visualize and Interact with Principal Coordinates Analysis Plots</description> 14 <description>Visualize and Interact with Principal Coordinates Analysis Plots</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container> 16 <container type="docker">quay.io/qiime2/core:2022.11</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version emperor</version_command> 18 <version_command>q2galaxy version emperor</version_command>
19 <command detect_errors="aggressive">q2galaxy run emperor plot '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run emperor plot '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required] The principal coordinates matrix to be plotted."> 24 <param name="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required] The principal coordinates matrix to be plotted.">
55 </section> 55 </section>
56 </inputs> 56 </inputs>
57 <outputs> 57 <outputs>
58 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 58 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
59 </outputs> 59 </outputs>
60 <tests/> 60 <tests>
61 <test>
62 <param name="pcoa" value="plot.test0.pcoa-result.qza" ftype="qza"/>
63 <repeat name="metadata">
64 <conditional name="__q2galaxy__GUI__conditional__metadata__">
65 <param name="type" value="tsv"/>
66 <param name="source" value="plot.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
67 </conditional>
68 </repeat>
69 <output name="visualization" ftype="qzv">
70 <assert_contents>
71 <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}\/metadata.yaml">
72 <has_line_matching expression="type: Visualization"/>
73 </has_archive_member>
74 </assert_contents>
75 </output>
76 </test>
77 </tests>
61 <help> 78 <help>
62 QIIME 2: emperor plot 79 QIIME 2: emperor plot
63 ===================== 80 =====================
64 Visualize and Interact with Principal Coordinates Analysis Plots 81 Visualize and Interact with Principal Coordinates Analysis Plots
65 82
72 89
73 Description: 90 Description:
74 ------------ 91 ------------
75 Generates an interactive ordination plot where the user can visually integrate sample metadata. 92 Generates an interactive ordination plot where the user can visually integrate sample metadata.
76 93
94 Examples:
95 ---------
96
97 emperor_plot
98 ************
99 Using the ``qiime2 emperor plot`` tool:
100 #. Set *"pcoa"* to ``#: pcoa-result.qza``
101 #. For *"metadata"*:
102
103 - Perform the following steps.
104
105 #. Leave as ``Metadata from TSV``
106 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
107
108
109 #. Press the ``Execute`` button.
110
111 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
112 (Renaming is optional, but it will make any subsequent steps easier to complete.)
113
114 .. list-table::
115 :align: left
116 :header-rows: 1
117
118 * - History Name
119 - *"Name"* to set (be sure to press ``Save``)
120 * - ``#: qiime2 emperor plot [...] : visualization.qzv``
121 - ``plot.qzv``
122
77 123
78 | 124 |
79 125
80 </help> 126 </help>
81 <citations> 127 <citations>