view qiime2__taxa__barplot.xml @ 3:0c992800a5cc draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?xml version='1.0' encoding='utf-8'?>
<!--
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: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 taxa barplot" id="qiime2__taxa__barplot" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Visualize taxonomy with an interactive bar plot</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version taxa</version_command>
    <command detect_errors="exit_code">q2galaxy run taxa barplot '$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]" 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]', '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">
                        <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="barplot.test0.table.qza" ftype="qza"/>
            <param name="taxonomy" value="barplot.test0.taxonomy.qza" ftype="qza"/>
            <repeat name="metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="barplot.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 barplot
=====================
Visualize taxonomy with an interactive bar plot


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
This visualizer produces an interactive barplot visualization of taxonomies. Interactive features include multi-level sorting, plot recoloring, sample relabeling, and SVG figure export.

Examples:
---------

barplot
*******
Using the ``qiime2 taxa barplot`` 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 barplot [...] : visualization.qzv``
      - ``taxa-bar-plots.qzv``


|  

</help>
    <citations>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>