annotate qiime2__rescript__get_eukaryome_data.xml @ 0:4fe476cce2f0 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-eukaryome-data" id="qiime2__rescript__get_eukaryome_data" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Download and import Eukaryome 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_eukaryome_data '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <repeat name="rrna_gene" min="1" help="[required]  Download the rRNA gene(s) of interest. Specify the respective gene(s), or download all genes using 'all'." title="rrna_gene: List[Str % Choices('SSU', 'LSU', 'ITS', 'longread', 'all')]">
            <param name="element" type="select" label="element: Str % Choices('SSU', 'LSU', 'ITS', 'longread', 'all')">
                <option value="__q2galaxy__::literal::None">Selection required</option>
                <option value="SSU">SSU</option>
                <option value="LSU">LSU</option>
                <option value="ITS">ITS</option>
                <option value="longread">longread</option>
                <option value="all">all</option>
                <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
            </param>
        </repeat>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="version" type="select" label="version: Str % Choices('1.9.4', '1.9.3', '1.9.2')" display="radio">
                <option value="1.9.4" selected="true">1.9.4</option>
                <option value="1.9.3">1.9.3</option>
                <option value="1.9.2">1.9.2</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <collection name="eukaryome_sequences" type="list">
            <discover_datasets directory="eukaryome_sequences" pattern="__name_and_ext__"/>
        </collection>
        <collection name="eukaryome_taxonomy" type="list">
            <discover_datasets directory="eukaryome_taxonomy" pattern="__name_and_ext__"/>
        </collection>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript get-eukaryome-data
====================================
Download and import Eukaryome reference data.


Outputs:
--------
:eukaryome_sequences.qza: Eukaryome reference sequence output directory.
:eukaryome_taxonomy.qza: Eukaryome reference taxonomy output directory.

|  

Description:
------------
Download and import a variety of rRNA gene sequences along with their associated taxonomy from the Eukaryome database. Simply provide the database version, the rRNA gene of interest, the reference sequence type, and if reference sequences with unspecified species information should be downloaded. NOTE: THIS ACTION ACQUIRES DATA FROM EUKARYOME. To learn more, please visit https://eukaryome.org/.


|  

</help>
    <citations>
        <citation type="doi">10.1093/database/baae043</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>