annotate qiime2__feature_table__summarize.xml @ 2:365ce7a8e641 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 65e4952f33eb335528e8553150e9097e5ea8f556

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 feature-table summarize" id="qiime2__feature_table__summarize" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Summarize table</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="exit_code">q2galaxy run feature_table summarize '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table to be summarized.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                <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">
            <repeat name="sample_metadata" help="[optional]  The sample metadata." title="sample_metadata: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
                    <param name="type" type="select" label="sample_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="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="summarize.test0.feature-table.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 summarize
================================
Summarize table


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

|  

Description:
------------
Generate visual and tabular summaries of a feature table.

Examples:
---------

feature_table_summarize
***********************
Using the ``qiime2 feature-table summarize`` tool:
 #. Set *"table"* to ``#: feature-table.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 summarize [...] : visualization.qzv``
      - ``table.qzv``


|  

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