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comparison qiime2__metadata__tabulate.xml @ 1:f6763a86190b draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:58:11 +0000
parents b85efa8e40a0
children d6e1b976c373
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0:b85efa8e40a0 1:f6763a86190b
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 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Interactively explore Metadata in an HTML table</description> 14 <description>Interactively explore Metadata in an HTML table</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 metadata</version_command> 18 <version_command>q2galaxy version metadata</version_command>
19 <command detect_errors="aggressive">q2galaxy run metadata tabulate '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run metadata tabulate '$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 <repeat name="input" min="1" help="[required] The metadata to tabulate." title="input: Metadata"> 24 <repeat name="input" min="1" help="[required] The metadata to tabulate." title="input: Metadata">
40 </section> 40 </section>
41 </inputs> 41 </inputs>
42 <outputs> 42 <outputs>
43 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 43 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
44 </outputs> 44 </outputs>
45 <tests/> 45 <tests>
46 <test>
47 <repeat name="input">
48 <conditional name="__q2galaxy__GUI__conditional__input__">
49 <param name="type" value="qza"/>
50 <param name="source" value="tabulate.test0.demux-stats.qza" ftype="qza"/>
51 </conditional>
52 </repeat>
53 <output name="visualization" ftype="qzv">
54 <assert_contents>
55 <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">
56 <has_line_matching expression="type: Visualization"/>
57 </has_archive_member>
58 </assert_contents>
59 </output>
60 </test>
61 <test>
62 <repeat name="input">
63 <conditional name="__q2galaxy__GUI__conditional__input__">
64 <param name="type" value="tsv"/>
65 <param name="source" value="tabulate.test1.sample-metadata.tsv" ftype="qiime2.tabular"/>
66 </conditional>
67 </repeat>
68 <repeat name="input">
69 <conditional name="__q2galaxy__GUI__conditional__input__">
70 <param name="type" value="qza"/>
71 <param name="source" value="tabulate.test1.faith-pd-vector.qza" ftype="qza"/>
72 </conditional>
73 </repeat>
74 <param name="page_size" value="25"/>
75 <output name="visualization" ftype="qzv">
76 <assert_contents>
77 <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">
78 <has_line_matching expression="type: Visualization"/>
79 </has_archive_member>
80 </assert_contents>
81 </output>
82 </test>
83 </tests>
46 <help> 84 <help>
47 QIIME 2: metadata tabulate 85 QIIME 2: metadata tabulate
48 ========================== 86 ==========================
49 Interactively explore Metadata in an HTML table 87 Interactively explore Metadata in an HTML table
50 88
57 95
58 Description: 96 Description:
59 ------------ 97 ------------
60 Generate a tabular view of Metadata. The output visualization supports interactive filtering, sorting, and exporting to common file formats. 98 Generate a tabular view of Metadata. The output visualization supports interactive filtering, sorting, and exporting to common file formats.
61 99
100 Examples:
101 ---------
102
103 basic_tabulate_usage
104 ********************
105 Using the ``qiime2 metadata tabulate`` tool:
106 #. For *"input"*:
107
108 - Perform the following steps.
109
110 #. Change to ``Metadata from Artifact``
111 #. Set *"Metadata Source"* to ``demux-stats.qza``
112
113
114 #. Press the ``Execute`` button.
115
116 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
117 (Renaming is optional, but it will make any subsequent steps easier to complete.)
118
119 .. list-table::
120 :align: left
121 :header-rows: 1
122
123 * - History Name
124 - *"Name"* to set (be sure to press ``Save``)
125 * - ``#: qiime2 metadata tabulate [...] : visualization.qzv``
126 - ``demux-stats-viz.qzv``
127
128 tabulate_multiple_files
129 ***********************
130 | Multiple metadata files or artifacts viewed as metadata can be merged to make one tabular visualization. This one displays only 25 metadata rows per page.
131 Using the ``qiime2 metadata tabulate`` tool:
132 #. For *"input"*:
133
134 #. Perform the following steps.
135
136 #. Leave as ``Metadata from TSV``
137 #. Set *"Metadata Source"* to ``sample-metadata.tsv``
138
139 #. Press the ``+ Insert input`` button to set up the next steps.
140
141 #. Change to ``Metadata from Artifact``
142 #. Set *"Metadata Source"* to ``faith-pd-vector.qza``
143
144
145 #. Expand the ``additional options`` section
146
147 - Set *"page_size"* to ``25``
148
149 #. Press the ``Execute`` button.
150
151 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
152 (Renaming is optional, but it will make any subsequent steps easier to complete.)
153
154 .. list-table::
155 :align: left
156 :header-rows: 1
157
158 * - History Name
159 - *"Name"* to set (be sure to press ``Save``)
160 * - ``#: qiime2 metadata tabulate [...] : visualization.qzv``
161 - ``demux-stats-viz.qzv``
162
62 163
63 | 164 |
64 165
65 </help> 166 </help>
66 <citations> 167 <citations>