annotate qiime2__deblur__visualize_stats.xml @ 3:d1b15724ff2b draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 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 deblur visualize-stats" id="qiime2__deblur__visualize_stats" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Visualize Deblur stats per sample.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version deblur</version_command>
    <command detect_errors="exit_code">q2galaxy run deblur visualize_stats '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="deblur_stats" type="data" format="qza" label="deblur_stats: DeblurStats" help="[required]  Summary statistics of the Deblur process.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="DeblurStats"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DeblurStats']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests>
        <test>
            <param name="deblur_stats" value="visualize_stats.test0.deblur-stats.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: deblur visualize-stats
===============================
Visualize Deblur stats per sample.


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

|  

Description:
------------
Display Deblur statistics per sample

Examples:
---------

visualize_stats
***************
Using the ``qiime2 deblur visualize-stats`` tool:
 #. Set *"deblur_stats"* to ``#: deblur-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 deblur visualize-stats [...] : visualization.qzv``
      - ``deblur-stats-viz.qzv``


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob},
 journal = {MSystems},
 number = {2},
 pages = {e00191--16},
 publisher = {Am Soc Microbiol},
 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
 volume = {2},
 year = {2017}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>