<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 rescript get-ncbi-genomes" id="qiime2__rescript__get_ncbi_genomes" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="taxon" type="text" label="taxon: Str" help="[required]  NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.">
            <sanitizer>
                <valid initial="string.printable"/>
            </sanitizer>
            <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank', 'all')" display="radio">
                <option value="refseq" selected="true">refseq</option>
                <option value="genbank">genbank</option>
                <option value="all">all</option>
            </param>
            <repeat name="assembly_levels" help="[default: ['complete_genome']]  Fetch only genome assemblies that are one of the specified assembly levels." title="assembly_levels: List[Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')]">
                <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio">
                    <option value="__q2galaxy__::literal::None">Selection required</option>
                    <option value="complete_genome">complete_genome</option>
                    <option value="chromosome">chromosome</option>
                    <option value="scaffold">scaffold</option>
                    <option value="contig">contig</option>
                    <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
                </param>
            </repeat>
            <param name="only_reference" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="only_reference: Bool" help="[default: Yes]  Fetch only reference and representative genome assemblies."/>
            <param name="only_genomic" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="only_genomic: Bool" help="[default: No]  Exclude plasmid, mitochondrial and chloroplast molecules from the final results (i.e., keep only genomic DNA)."/>
            <param name="tax_exact_match" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="tax_exact_match: Bool" help="[default: No]  If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too."/>
            <param name="page_size" type="integer" min="20" max="1000" value="20" label="page_size: Int % Range(20, 1000, inclusive_end=True)" help="[default: 20]  The maximum number of genome assemblies to return per request. If number of genomes to fetch is higher than this number, requests will be repeated until all assemblies are fetched."/>
            <repeat name="ranks" help="[default: ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']]  List of taxonomic ranks for building a taxonomy from the NCBI Taxonomy database." title="ranks: List[Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')]">
                <param name="element" type="select" label="element: Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'cohort', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species group', 'species subgroup', 'species', 'subspecies', 'forma')">
                    <option value="__q2galaxy__::literal::None">Selection required</option>
                    <option value="domain">domain</option>
                    <option value="superkingdom">superkingdom</option>
                    <option value="kingdom">kingdom</option>
                    <option value="subkingdom">subkingdom</option>
                    <option value="superphylum">superphylum</option>
                    <option value="phylum">phylum</option>
                    <option value="subphylum">subphylum</option>
                    <option value="infraphylum">infraphylum</option>
                    <option value="superclass">superclass</option>
                    <option value="class">class</option>
                    <option value="subclass">subclass</option>
                    <option value="infraclass">infraclass</option>
                    <option value="cohort">cohort</option>
                    <option value="superorder">superorder</option>
                    <option value="order">order</option>
                    <option value="suborder">suborder</option>
                    <option value="infraorder">infraorder</option>
                    <option value="parvorder">parvorder</option>
                    <option value="superfamily">superfamily</option>
                    <option value="family">family</option>
                    <option value="subfamily">subfamily</option>
                    <option value="tribe">tribe</option>
                    <option value="subtribe">subtribe</option>
                    <option value="genus">genus</option>
                    <option value="subgenus">subgenus</option>
                    <option value="species group">species group</option>
                    <option value="species subgroup">species subgroup</option>
                    <option value="species">species</option>
                    <option value="subspecies">subspecies</option>
                    <option value="forma">forma</option>
                    <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
                </param>
            </repeat>
            <param name="rank_propagation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="rank_propagation: Bool" help="[default: Yes]  If a rank has no taxonomy associated with it, the taxonomy from the upper-level rank of that lineage, will be propagated downward. For example, if we are missing the genus label for 'f__Pasteurellaceae; g__'then the 'f__' rank will be propagated to become: 'f__Pasteurellaceae; g__Pasteurellaceae'."/>
        </section>
    </inputs>
    <outputs>
        <data name="genome_assemblies" format="qza" label="${tool.name} on ${on_string}: genome_assemblies.qza" from_work_dir="genome_assemblies.qza"/>
        <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/>
        <data name="proteins" format="qza" label="${tool.name} on ${on_string}: proteins.qza" from_work_dir="proteins.qza"/>
        <data name="taxonomies" format="qza" label="${tool.name} on ${on_string}: taxonomies.qza" from_work_dir="taxonomies.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript get-ncbi-genomes
==================================
Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.


Outputs:
--------
:genome_assemblies.qza: Nucleotide sequences of requested genomes.
:loci.qza: Loci features of requested genomes.
:proteins.qza: Protein sequences originating from requested genomes.
:taxonomies.qza: Taxonomies of requested genomes.

|  

Description:
------------
Uses NCBI Datasets to fetch genomes for indicated taxa. Nucleotide sequences and protein/gene annotations will be fetched and supplemented with full taxonomy of every sequence.


|  

</help>
    <citations>
        <citation type="doi">10.1093/nar/gkv1276</citation>
        <citation type="doi">10.1093/nar/gkv1189</citation>
        <citation type="doi">10.1093/database/baaa062</citation>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>