Mercurial > repos > q2d2 > qiime2__feature_table__group
diff 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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--- a/qiime2__feature_table__group.xml Mon Aug 29 19:54:40 2022 +0000 +++ b/qiime2__feature_table__group.xml Fri Jan 13 22:55:48 2023 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<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"> +<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"> <description>Group samples or features by a metadata column</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version feature_table</version_command> - <command detect_errors="aggressive">q2galaxy run feature_table group '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run feature_table group '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -62,7 +62,25 @@ <outputs> <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/> </outputs> - <tests/> + <tests> + <test> + <param name="table" value="group.test0.feature-table.qza" ftype="qza"/> + <param name="axis" value="sample"/> + <conditional name="metadata"> + <param name="type" value="tsv"/> + <param name="source" value="group.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> + <param name="column" value="3"/> + </conditional> + <param name="mode" value="median-ceiling"/> + <output name="grouped_table" ftype="qza"> + <assert_contents> + <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"> + <has_line_matching expression="type: FeatureTable\[Frequency\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: feature-table group ============================ @@ -79,6 +97,36 @@ ------------ Group samples or features in a feature table using metadata to define the mapping of IDs to a group. +Examples: +--------- + +group_samples +************* +| 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. +Using the ``qiime2 feature-table group`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"axis"* to ``sample`` + #. For *"metadata"*: + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + #. Set *"Column Name"* to ``body-site`` + + #. Set *"mode"* to ``median-ceiling`` + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 feature-table group [...] : grouped_table.qza`` + - ``body-site-table.qza`` + |