Mercurial > repos > q2d2 > qiime2__taxa__barplot2
changeset 0:50bcca67ad6a draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:32:49 +0000 |
| parents | |
| children | |
| files | qiime2__taxa__barplot2.xml test-data/barplot.test0.sample-metadata.tsv test-data/barplot.test0.table.qza test-data/barplot.test0.taxonomy.qza test-data/barplot2.test0.sample-metadata.tsv test-data/barplot2.test0.table.qza test-data/barplot2.test0.taxonomy.qza test-data/collapse.test0.table.qza test-data/collapse.test0.taxonomy.qza |
| diffstat | 9 files changed, 224 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__taxa__barplot2.xml Sat Nov 01 17:32:49 2025 +0000 @@ -0,0 +1,152 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2025, 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) +for: + qiime2 (version: 2025.10.0) +--> +<tool name="qiime2 taxa barplot2" id="qiime2__taxa__barplot2" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Experimental interactive stacked bar plot of per-sample taxa.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> + </requirements> + <version_command>q2galaxy version taxa</version_command> + <command detect_errors="exit_code">q2galaxy run taxa barplot2 '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]" 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]"/> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</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"> + <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> + <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> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests> + <test> + <param name="table" value="barplot2.test0.table.qza" ftype="qza"/> + <param name="taxonomy" value="barplot2.test0.taxonomy.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="barplot2.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <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: taxa barplot2 +====================== +Experimental interactive stacked bar plot of per-sample taxa. + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +This is an early release of a replacement for the `barplot` visualizer in this plugin. As of 2025.10, this should be considered experimental, and we are very interested in community feedback on this new visualizer. This command will eventually be removed when this visualizer replaces the `barplot` visualizer. + +Examples: +--------- + +barplot +******* +Using the ``qiime2 taxa barplot2`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Expand the ``additional options`` section + + #. Set *"taxonomy"* to ``#: taxonomy.qza`` + #. For *"metadata"*: + + - Press the ``+ Insert metadata`` button to set up the next steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + + + + #. 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 taxa barplot2 [...] : visualization.qzv`` + - ``taxa-bar-plots.qzv`` + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barplot.test0.sample-metadata.tsv Sat Nov 01 17:32:49 2025 +0000 @@ -0,0 +1,36 @@ +sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start +#q2:types categorical categorical numeric numeric numeric categorical categorical numeric +L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0 +L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84 +L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112 +L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140 +L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84 +L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112 +L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140 +L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168 +L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0 +L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84 +L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112 +L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140 +L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168 +L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0 +L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84 +L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112 +L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140 +L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168 +L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0 +L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84 +L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140 +L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168 +L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0 +L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84 +L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140 +L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168 +L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0 +L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84 +L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140 +L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168 +L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0 +L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84 +L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140 +L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barplot2.test0.sample-metadata.tsv Sat Nov 01 17:32:49 2025 +0000 @@ -0,0 +1,36 @@ +sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start +#q2:types categorical categorical numeric numeric numeric categorical categorical numeric +L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0 +L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84 +L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112 +L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140 +L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84 +L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112 +L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140 +L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168 +L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0 +L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84 +L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112 +L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140 +L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168 +L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0 +L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84 +L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112 +L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140 +L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168 +L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0 +L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84 +L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140 +L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168 +L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0 +L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84 +L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140 +L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168 +L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0 +L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84 +L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140 +L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168 +L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0 +L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84 +L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140 +L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168