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comparison qiime2__feature_table__summarize.xml @ 1:c7553080ec2e draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:52:35 +0000
parents bfe9f18ac641
children 365ce7a8e641
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0:bfe9f18ac641 1:c7553080ec2e
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 feature-table summarize" id="qiime2__feature_table__summarize" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Summarize table</description> 14 <description>Summarize 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 feature_table</version_command> 18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="aggressive">q2galaxy run feature_table summarize '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run feature_table summarize '$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="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table to be summarized."> 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table to be summarized.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
27 <filter type="add_value" value="FeatureTable[Frequency]"/>
26 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> 28 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
27 <filter type="add_value" value="FeatureTable[Frequency]"/>
28 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
29 </options> 29 </options>
30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> 30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
31 </param> 31 </param>
32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 32 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
33 <repeat name="sample_metadata" help="[optional] The sample metadata." title="sample_metadata: Metadata"> 33 <repeat name="sample_metadata" help="[optional] The sample metadata." title="sample_metadata: Metadata">
47 </section> 47 </section>
48 </inputs> 48 </inputs>
49 <outputs> 49 <outputs>
50 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> 50 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
51 </outputs> 51 </outputs>
52 <tests/> 52 <tests>
53 <test>
54 <param name="table" value="summarize.test0.feature-table.qza" ftype="qza"/>
55 <output name="visualization" ftype="qzv">
56 <assert_contents>
57 <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">
58 <has_line_matching expression="type: Visualization"/>
59 </has_archive_member>
60 </assert_contents>
61 </output>
62 </test>
63 </tests>
53 <help> 64 <help>
54 QIIME 2: feature-table summarize 65 QIIME 2: feature-table summarize
55 ================================ 66 ================================
56 Summarize table 67 Summarize table
57 68
64 75
65 Description: 76 Description:
66 ------------ 77 ------------
67 Generate visual and tabular summaries of a feature table. 78 Generate visual and tabular summaries of a feature table.
68 79
80 Examples:
81 ---------
82
83 feature_table_summarize
84 ***********************
85 Using the ``qiime2 feature-table summarize`` tool:
86 #. Set *"table"* to ``#: feature-table.qza``
87 #. Press the ``Execute`` button.
88
89 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
90 (Renaming is optional, but it will make any subsequent steps easier to complete.)
91
92 .. list-table::
93 :align: left
94 :header-rows: 1
95
96 * - History Name
97 - *"Name"* to set (be sure to press ``Save``)
98 * - ``#: qiime2 feature-table summarize [...] : visualization.qzv``
99 - ``table.qzv``
100
69 101
70 | 102 |
71 103
72 </help> 104 </help>
73 <citations> 105 <citations>