annotate qiime2__feature_table__summarize_plus.xml @ 0:4954486b6f4c draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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 feature-table summarize-plus" id="qiime2__feature_table__summarize_plus" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Summarize table plus</description>
    <requirements>
        <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 summarize_plus '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence]" help="[required]  The feature table to be summarized.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <repeat name="metadata" help="[optional]  The sample metadata." title="metadata: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" type="select" label="metadata: Metadata">
                        <option value="tsv" selected="true">Metadata from TSV</option>
                        <option value="qza">Metadata from Artifact</option>
                    </param>
                    <when value="tsv">
                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                    </when>
                    <when value="qza">
                        <param name="source" type="data" format="qza" label="Metadata Source"/>
                    </when>
                </conditional>
            </repeat>
        </section>
    </inputs>
    <outputs>
        <data name="feature_frequencies" format="qza" label="${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_plus.test0.feature-table.qza" ftype="qza"/>
            <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"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: feature-table summarize-plus
=====================================
Summarize table plus


Outputs:
--------
: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. Tabulate sample and feature frequencies.

Examples:
---------

feature_table_summarize_plus
****************************
Using the ``qiime2 feature-table summarize-plus`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Press the ``Execute`` button.

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::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 feature-table summarize-plus [...] : feature_frequencies.qza``
      - ``feature-frequencies.qza``
    * - ``#: qiime2 feature-table summarize-plus [...] : sample_frequencies.qza``
      - ``sample-frequencies.qza``
    * - ``#: qiime2 feature-table summarize-plus [...] : summary.qzv``
      - ``visual summary.qzv``


|  

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