Mercurial > repos > q2d2 > qiime2__feature_table__summarize
comparison qiime2__feature_table__summarize.xml @ 1:c7553080ec2e draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:52:35 +0000 |
parents | bfe9f18ac641 |
children | 365ce7a8e641 |
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0:bfe9f18ac641 | 1:c7553080ec2e |
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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> |