view qiime2__rescript__get_unite_data.xml @ 3:b8c417ff73b7 draft default tip

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

<?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-unite-data" id="qiime2__rescript__get_unite_data" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Download and import UNITE 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_unite_data '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="version" type="select" label="version: Str % Choices('2025-02-19', '2024-04-04', '2023-07-18', '2022-10-16', '2021-05-10', '2020-02-20')">
                <option value="2025-02-19" selected="true">2025-02-19</option>
                <option value="2024-04-04">2024-04-04</option>
                <option value="2023-07-18">2023-07-18</option>
                <option value="2022-10-16">2022-10-16</option>
                <option value="2021-05-10">2021-05-10</option>
                <option value="2020-02-20">2020-02-20</option>
            </param>
            <param name="taxon_group" type="select" label="taxon_group: Str % Choices('fungi', 'eukaryotes')" display="radio">
                <option value="fungi">fungi</option>
                <option value="eukaryotes" selected="true">eukaryotes</option>
            </param>
            <param name="cluster_id" type="select" label="cluster_id: Str % Choices('99', '97', 'dynamic')" display="radio">
                <option value="99" selected="true">99</option>
                <option value="97">97</option>
                <option value="dynamic">dynamic</option>
            </param>
            <param name="singletons" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="singletons: Bool" help="[default: No]  Include singleton clusters in the database."/>
        </section>
    </inputs>
    <outputs>
        <data name="taxonomy" format="qza" label="${tool.name} on ${on_string}: taxonomy.qza" from_work_dir="taxonomy.qza"/>
        <data name="sequences" format="qza" label="${tool.name} on ${on_string}: sequences.qza" from_work_dir="sequences.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript get-unite-data
================================
Download and import UNITE reference data.


Outputs:
--------
:taxonomy.qza: UNITE reference taxonomy.
:sequences.qza: UNITE reference sequences.

|  

Description:
------------
Download and import ITS sequences and taxonomy from the UNITE database, given a version number and taxon_group, with the option to select a cluster_id and include singletons. Downloads data directly from UNITE's PlutoF REST API. NOTE: THIS ACTION ACQUIRES DATA FROM UNITE, which is licensed under CC BY-SA 4.0. To learn more, please visit https://unite.ut.ee/cite.php and https://creativecommons.org/licenses/by-sa/4.0/.


|  

</help>
    <citations>
        <citation type="doi">10.1093/nar/gky1022</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>