Mercurial > repos > q2d2 > qiime2__feature_table__summarize
changeset 9:41e9af5ca46b draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 36ec48f8c55799a0c963733df13da30f19b1bdf3
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--- a/qiime2__feature_table__summarize.xml Sat Nov 01 17:20:38 2025 +0000 +++ b/qiime2__feature_table__summarize.xml Wed Jan 28 16:26:59 2026 +0000 @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2025, QIIME 2 development team. +Copyright (c) 2026, 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: 2025.10.0) + q2galaxy (version: 2026.1.0) for: - qiime2 (version: 2025.10.0) + qiime2 (version: 2026.1.0) --> -<tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2026.1.0+q2galaxy.2026.1.0" profile="22.05" license="BSD-3-Clause"> <description>Summarize table</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.10</container> + <container type="docker">quay.io/qiime2/amplicon:2026.1</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table summarize '$inputs'</command> @@ -32,9 +32,9 @@ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> - <repeat name="sample_metadata" help="[optional] The sample metadata." title="sample_metadata: Metadata"> - <conditional name="__q2galaxy__GUI__conditional__sample_metadata__"> - <param name="type" type="select" label="sample_metadata: Metadata"> + <repeat name="metadata" help="[optional] The sample metadata." title="metadata: Metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" type="select" label="metadata: Metadata"> <option value="tsv" selected="true">Metadata from TSV</option> <option value="qza">Metadata from Artifact</option> </param> @@ -49,12 +49,28 @@ </section> </inputs> <outputs> - <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + <data name="feature_frequencies" format="qza" label="${tool.name} on ${on_string}: feature_frequencies.qza" from_work_dir="feature_frequencies.qza"/> + <data name="sample_frequencies" format="qza" label="${tool.name} on ${on_string}: sample_frequencies.qza" from_work_dir="sample_frequencies.qza"/> + <data name="summary" format="qzv" label="${tool.name} on ${on_string}: summary.qzv" from_work_dir="summary.qzv"/> </outputs> <tests> <test> <param name="table" value="summarize.test0.feature-table.qza" ftype="qza"/> - <output name="visualization" ftype="qzv"> + <output name="feature_frequencies" 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: ImmutableMetadata"/> + </has_archive_member> + </assert_contents> + </output> + <output name="sample_frequencies" 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: ImmutableMetadata"/> + </has_archive_member> + </assert_contents> + </output> + <output name="summary" ftype="qzv"> <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: Visualization"/> @@ -71,24 +87,26 @@ Outputs: -------- -:visualization.qzv: <no description> +:feature_frequencies.qza: Per-sample and total frequencies per feature. +:sample_frequencies.qza: Observed feature count and total frequencies per sample. +:summary.qzv: Visual summary of feature table | Description: ------------ -Generate visual and tabular summaries of a feature table. +Generate visual and tabular summaries of a feature table. Tabulate sample and feature frequencies. Examples: --------- -feature_table_summarize -*********************** +feature_table_summarize_ +************************ Using the ``qiime2 feature-table summarize`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Press the ``Execute`` button. -Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: +Once completed, for each 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:: @@ -97,8 +115,12 @@ * - History Name - *"Name"* to set (be sure to press ``Save``) - * - ``#: qiime2 feature-table summarize [...] : visualization.qzv`` - - ``table.qzv`` + * - ``#: qiime2 feature-table summarize [...] : feature_frequencies.qza`` + - ``feature-frequencies.qza`` + * - ``#: qiime2 feature-table summarize [...] : sample_frequencies.qza`` + - ``sample-frequencies.qza`` + * - ``#: qiime2 feature-table summarize [...] : summary.qzv`` + - ``visual summary.qzv`` |