Mercurial > repos > q2d2 > qiime2__feature_table__tabulate_seqs
changeset 3:2feea4c63f4c draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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--- a/qiime2__feature_table__tabulate_seqs.xml Thu Jun 08 19:44:24 2023 +0000 +++ b/qiime2__feature_table__tabulate_seqs.xml Thu Apr 25 21:11:45 2024 +0000 @@ -1,33 +1,59 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +Copyright (c) 2024, 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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>View sequence associated with each feature</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[AlignedSequence]"/> <filter type="add_value" value="FeatureData[Sequence]"/> - <filter type="add_value" value="FeatureData[AlignedSequence]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator> </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: Collection[FeatureData[Taxonomy]]" help="[optional] The taxonomic classifications of the tabulated features." multiple="true"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Taxonomy]"/> + </options> + </param> + <repeat name="metadata" help="[optional] Any additional metadata for the tabulated features." 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> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + </when> + </conditional> + </repeat> + <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio"> + <option value="strict" selected="true">strict</option> + <option value="union">union</option> + <option value="intersect">intersect</option> + </param> + </section> </inputs> <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> @@ -43,6 +69,28 @@ </assert_contents> </output> </test> + <test> + <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/> + <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/> + <output name="visualization" 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"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <test> + <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/> + <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/> + <output name="visualization" 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"/> + </has_archive_member> + </assert_contents> + </output> + </test> </tests> <help> QIIME 2: feature-table tabulate-seqs @@ -81,6 +129,50 @@ * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv`` - ``rep-seqs.qzv`` +feature_table_tabulate_seqs_single_taxon +**************************************** +Using the ``qiime2 feature-table tabulate-seqs`` tool: + #. Set *"data"* to ``#: rep-seqs-single-taxon.qza`` + #. Expand the ``additional options`` section + + - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']`` + + #. 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 tabulate-seqs [...] : visualization.qzv`` + - ``rep-seqs.qzv`` + +feature_table_tabulate_seqs_multi_taxon +*************************************** +Using the ``qiime2 feature-table tabulate-seqs`` tool: + #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza`` + #. Expand the ``additional options`` section + + - Set *"taxonomy"* to ``#: multi-taxonomy/`` + + #. 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 tabulate-seqs [...] : visualization.qzv`` + - ``rep-seqs.qzv`` + |