annotate qiime2__rescript__get_gtdb_data.xml @ 5:2e21090728f2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 rescript get-gtdb-data" id="qiime2__rescript__get_gtdb_data" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Download, parse, and import SSU GTDB reference data.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript get_gtdb_data '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="version" type="select" label="version: Str % Choices('202.0', '207.0', '214.0', '214.1', '220.0', '226.0')">
                <option value="202.0">202.0</option>
                <option value="207.0">207.0</option>
                <option value="214.0">214.0</option>
                <option value="214.1">214.1</option>
                <option value="220.0">220.0</option>
                <option value="226.0" selected="true">226.0</option>
            </param>
            <param name="domain" type="select" label="domain: Str % Choices('Both', 'Bacteria', 'Archaea')" display="radio">
                <option value="Both" selected="true">Both</option>
                <option value="Bacteria">Bacteria</option>
                <option value="Archaea">Archaea</option>
            </param>
            <param name="db_type" type="select" label="db_type: Str % Choices('All', 'SpeciesReps')" display="radio">
                <option value="All">All</option>
                <option value="SpeciesReps" selected="true">SpeciesReps</option>
            </param>
            <param name="url_type" type="select" label="url_type: Str % Choices('Primary', 'Mirror')" display="radio">
                <option value="Primary" selected="true">Primary</option>
                <option value="Mirror">Mirror</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="gtdb_taxonomy" format="qza" label="${tool.name} on ${on_string}: gtdb_taxonomy.qza" from_work_dir="gtdb_taxonomy.qza"/>
        <data name="gtdb_sequences" format="qza" label="${tool.name} on ${on_string}: gtdb_sequences.qza" from_work_dir="gtdb_sequences.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript get-gtdb-data
===============================
Download, parse, and import SSU GTDB reference data.


Outputs:
--------
:gtdb_taxonomy.qza: SSU GTDB reference taxonomy.
:gtdb_sequences.qza: SSU GTDB reference sequences.

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Description:
------------
Download, parse, and import SSU GTDB files, given a version number. Downloads data directly from GTDB, parses the taxonomy files, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM GTDB. SEE https://gtdb.ecogenomic.org/about FOR MORE INFORMATION and be aware that earlier versions may be released under a different license.


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</help>
    <citations>
        <citation type="doi">10.1038/s41587-020-0501-8</citation>
        <citation type="doi">10.1093/nar/gkab776</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>