annotate qiime2__metadata__tabulate.xml @ 1:f6763a86190b draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit 69da7976573cc07a363ac66bdacc9269d7cd3732

<?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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Interactively explore Metadata in an HTML table</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version metadata</version_command>
    <command detect_errors="exit_code">q2galaxy run metadata tabulate '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <repeat name="input" min="1" help="[required]  The metadata to tabulate." title="input: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__input__">
                <param name="type" type="select" label="input: Metadata">
                    <option value="tsv" selected="true">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="tsv">
                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="page_size" type="integer" value="100" label="page_size: Int" help="[default: 100]  The maximum number of Metadata records to display per page"/>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests>
        <test>
            <repeat name="input">
                <conditional name="__q2galaxy__GUI__conditional__input__">
                    <param name="type" value="qza"/>
                    <param name="source" value="tabulate.test0.demux-stats.qza" ftype="qza"/>
                </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>
        <test>
            <repeat name="input">
                <conditional name="__q2galaxy__GUI__conditional__input__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="tabulate.test1.sample-metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <repeat name="input">
                <conditional name="__q2galaxy__GUI__conditional__input__">
                    <param name="type" value="qza"/>
                    <param name="source" value="tabulate.test1.faith-pd-vector.qza" ftype="qza"/>
                </conditional>
            </repeat>
            <param name="page_size" value="25"/>
            <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: metadata tabulate
==========================
Interactively explore Metadata in an HTML table


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

|  

Description:
------------
Generate a tabular view of Metadata. The output visualization supports interactive filtering, sorting, and exporting to common file formats.

Examples:
---------

basic_tabulate_usage
********************
Using the ``qiime2 metadata tabulate`` tool:
 #. For *"input"*:

    - Perform the following steps.

      #. Change to ``Metadata from Artifact``
      #. Set *"Metadata Source"* to ``demux-stats.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 metadata tabulate [...] : visualization.qzv``
      - ``demux-stats-viz.qzv``

tabulate_multiple_files
***********************
| Multiple metadata files or artifacts viewed as metadata can be merged to make one tabular visualization. This one displays only 25 metadata rows per page.
Using the ``qiime2 metadata tabulate`` tool:
 #. For *"input"*:

    #. Perform the following steps.

       #. Leave as ``Metadata from TSV``
       #. Set *"Metadata Source"* to ``sample-metadata.tsv``

    #. Press the ``+ Insert input`` button to set up the next steps.

       #. Change to ``Metadata from Artifact``
       #. Set *"Metadata Source"* to ``faith-pd-vector.qza``


 #. Expand the ``additional options`` section

    - Set *"page_size"* to ``25``

 #. 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 metadata tabulate [...] : visualization.qzv``
      - ``demux-stats-viz.qzv``


|  

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