Mercurial > repos > q2d2 > qiime2__feature_table__group
comparison qiime2__feature_table__group.xml @ 1:94617586f2cb 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 22:55:48 +0000 |
parents | 834bb534ba6d |
children | a27ceaf4cfc2 |
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0:834bb534ba6d | 1:94617586f2cb |
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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 group" id="qiime2__feature_table__group" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | 13 <tool name="qiime2 feature-table group" id="qiime2__feature_table__group" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> |
14 <description>Group samples or features by a metadata column</description> | 14 <description>Group samples or features by a metadata column</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 group '$inputs'</command> | 19 <command detect_errors="exit_code">q2galaxy run feature_table group '$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]" help="[required] The table to group samples or features on."> | 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The table to group samples or features on."> |
60 </param> | 60 </param> |
61 </inputs> | 61 </inputs> |
62 <outputs> | 62 <outputs> |
63 <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/> | 63 <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/> |
64 </outputs> | 64 </outputs> |
65 <tests/> | 65 <tests> |
66 <test> | |
67 <param name="table" value="group.test0.feature-table.qza" ftype="qza"/> | |
68 <param name="axis" value="sample"/> | |
69 <conditional name="metadata"> | |
70 <param name="type" value="tsv"/> | |
71 <param name="source" value="group.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> | |
72 <param name="column" value="3"/> | |
73 </conditional> | |
74 <param name="mode" value="median-ceiling"/> | |
75 <output name="grouped_table" ftype="qza"> | |
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: FeatureTable\[Frequency\]"/> | |
79 </has_archive_member> | |
80 </assert_contents> | |
81 </output> | |
82 </test> | |
83 </tests> | |
66 <help> | 84 <help> |
67 QIIME 2: feature-table group | 85 QIIME 2: feature-table group |
68 ============================ | 86 ============================ |
69 Group samples or features by a metadata column | 87 Group samples or features by a metadata column |
70 | 88 |
77 | 95 |
78 Description: | 96 Description: |
79 ------------ | 97 ------------ |
80 Group samples or features in a feature table using metadata to define the mapping of IDs to a group. | 98 Group samples or features in a feature table using metadata to define the mapping of IDs to a group. |
81 | 99 |
100 Examples: | |
101 --------- | |
102 | |
103 group_samples | |
104 ************* | |
105 | Combine samples from the same body-site into single sample. Feature frequencies will be the median across the samples being combined, rounded up to the nearest whole number. | |
106 Using the ``qiime2 feature-table group`` tool: | |
107 #. Set *"table"* to ``#: feature-table.qza`` | |
108 #. Set *"axis"* to ``sample`` | |
109 #. For *"metadata"*: | |
110 | |
111 #. Leave as ``Metadata from TSV`` | |
112 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` | |
113 #. Set *"Column Name"* to ``body-site`` | |
114 | |
115 #. Set *"mode"* to ``median-ceiling`` | |
116 #. Press the ``Execute`` button. | |
117 | |
118 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: | |
119 (Renaming is optional, but it will make any subsequent steps easier to complete.) | |
120 | |
121 .. list-table:: | |
122 :align: left | |
123 :header-rows: 1 | |
124 | |
125 * - History Name | |
126 - *"Name"* to set (be sure to press ``Save``) | |
127 * - ``#: qiime2 feature-table group [...] : grouped_table.qza`` | |
128 - ``body-site-table.qza`` | |
129 | |
82 | 130 |
83 | | 131 | |
84 | 132 |
85 </help> | 133 </help> |
86 <citations> | 134 <citations> |