Mercurial > repos > q2d2 > qiime2__taxa__barplot
changeset 2:124673b2e9e7 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 65e4952f33eb335528e8553150e9097e5ea8f556
| author | q2d2 |
|---|---|
| date | Thu, 08 Jun 2023 19:52:38 +0000 |
| parents | 5750bac5b744 |
| children | 0c992800a5cc |
| files | qiime2__taxa__barplot.xml test-data/barplot.test0.table.qza test-data/barplot.test0.taxonomy.qza test-data/collapse.test0.table.qza test-data/collapse.test0.taxonomy.qza |
| diffstat | 5 files changed, 34 insertions(+), 17 deletions(-) [+] |
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--- a/qiime2__taxa__barplot.xml Fri Jan 13 23:01:20 2023 +0000 +++ b/qiime2__taxa__barplot.xml Thu Jun 08 19:52:38 2023 +0000 @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.11.1) + q2galaxy (version: 2023.5.0) for: - qiime2 (version: 2022.11.1) + qiime2 (version: 2023.5.1) --> -<tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Visualize taxonomy with an interactive bar plot</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.11</container> + <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version taxa</version_command> <command detect_errors="exit_code">q2galaxy run taxa barplot '$inputs'</command> @@ -21,19 +21,20 @@ <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> - <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table to visualize at various taxonomic levels."> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence]" help="[required] Feature table to visualize at various taxonomic levels."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> <filter type="add_value" value="FeatureTable[Frequency]"/> </options> - <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> - </param> - <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored."> - <options options_filter_attribute="metadata.semantic_type"> - <filter type="add_value" value="FeatureData[Taxonomy]"/> - </options> - <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> + <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"> + <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: FeatureData[Taxonomy]" help="[optional] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. If no taxonomy is provided, the feature IDs will be used as labels."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Taxonomy]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> + </param> <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"> @@ -48,6 +49,22 @@ </when> </conditional> </repeat> + <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional] Attempt to parse hierarchical taxonomic information from feature IDs by separating levels with this character. This parameter is ignored if a taxonomy is provided as input."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="level_delimiter" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> </section> </inputs> <outputs> @@ -95,15 +112,15 @@ ******* Using the ``qiime2 taxa barplot`` tool: #. Set *"table"* to ``#: table.qza`` - #. Set *"taxonomy"* to ``#: taxonomy.qza`` #. Expand the ``additional options`` section - - For *"metadata"*: + #. Set *"taxonomy"* to ``#: taxonomy.qza`` + #. For *"metadata"*: - - Press the ``+ Insert metadata`` button to set up the next steps. + - Press the ``+ Insert metadata`` button to set up the next steps. - #. Leave as ``Metadata from TSV`` - #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv``