comparison qiime2__rescript__get_pr2_data.xml @ 0:b37a81a7d407 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit b1fccfb38b4873cd4699743033449014a2978e7d

0:b37a81a7d407

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.4.0)
for:
    qiime2 (version: 2025.4.0)
-->
<tool name="qiime2 rescript get-pr2-data" id="qiime2__rescript__get_pr2_data" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Download, parse, and import SSU PR2 reference data.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript get_pr2_data '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="version" type="select" label="version: Str % Choices('5.0.0', '4.14.0')" display="radio">
                <option value="5.0.0" selected="true">5.0.0</option>
                <option value="4.14.0">4.14.0</option>
            </param>
            <repeat name="ranks" help="[optional]  List of taxonomic ranks for building a taxonomy from the PR2 Taxonomy database. Ranks can be provided as multiple separate flags, e.g.: `--p-ranks genus --p-ranks species`, or with a single flag delimited by a space: `--p-ranks genus species`. [default: 'domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species']" title="ranks: List[Str % Choices('domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species')]">
                <param name="element" type="select" label="element: Str % Choices('domain', 'supergroup', 'division', 'subdivision', 'class', 'order', 'family', 'genus', 'species')">
                    <option value="__q2galaxy__::literal::None">Selection required</option>
                    <option value="domain">domain</option>
                    <option value="supergroup">supergroup</option>
                    <option value="division">division</option>
                    <option value="subdivision">subdivision</option>
                    <option value="class">class</option>
                    <option value="order">order</option>
                    <option value="family">family</option>
                    <option value="genus">genus</option>
                    <option value="species">species</option>
                    <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
                </param>
            </repeat>
        </section>
    </inputs>
    <outputs>
        <data name="pr2_sequences" format="qza" label="${tool.name} on ${on_string}: pr2_sequences.qza" from_work_dir="pr2_sequences.qza"/>
        <data name="pr2_taxonomy" format="qza" label="${tool.name} on ${on_string}: pr2_taxonomy.qza" from_work_dir="pr2_taxonomy.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript get-pr2-data
==============================
Download, parse, and import SSU PR2 reference data.


Outputs:
--------
:pr2_sequences.qza: SSU PR2 reference sequences.
:pr2_taxonomy.qza: SSU PR2 reference taxonomy.

|  

Description:
------------
Download, parse, and import SSU PR2 files, given a version number. Downloads data directly from PR2, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM PR2, which is licensed under MIT. To learn more, please visit https://pr2-database.org/ and https://github.com/pr2database/.


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</help>
    <citations>
        <citation type="doi">10.1093/nar/gks1160</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>