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date Mon, 03 Jun 2024 23:30:45 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 rescript get-ncbi-genomes" id="qiime2__rescript__get_ncbi_genomes" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version rescript</version_command>
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19 <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="taxon" type="text" label="taxon: Str" help="[required] NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.">
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25 <sanitizer>
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26 <valid initial="string.printable"/>
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27 </sanitizer>
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28 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank')" display="radio">
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32 <option value="refseq" selected="true">refseq</option>
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33 <option value="genbank">genbank</option>
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34 </param>
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35 <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')]">
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36 <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio">
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37 <option value="__q2galaxy__::literal::None">Selection required</option>
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38 <option value="complete_genome">complete_genome</option>
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39 <option value="chromosome">chromosome</option>
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40 <option value="scaffold">scaffold</option>
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41 <option value="contig">contig</option>
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42 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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43 </param>
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44 </repeat>
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45 <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."/>
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46 <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."/>
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47 <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."/>
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48 </section>
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49 </inputs>
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50 <outputs>
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51 <data name="genome_assemblies" format="qza" label="${tool.name} on ${on_string}: genome_assemblies.qza" from_work_dir="genome_assemblies.qza"/>
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52 <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/>
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53 <data name="proteins" format="qza" label="${tool.name} on ${on_string}: proteins.qza" from_work_dir="proteins.qza"/>
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54 <data name="taxonomies" format="qza" label="${tool.name} on ${on_string}: taxonomies.qza" from_work_dir="taxonomies.qza"/>
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55 </outputs>
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56 <tests/>
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57 <help>
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58 QIIME 2: rescript get-ncbi-genomes
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59 ==================================
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60 Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
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61
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62
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63 Outputs:
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64 --------
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65 :genome_assemblies.qza: Nucleotide sequences of requested genomes.
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66 :loci.qza: Loci features of requested genomes.
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67 :proteins.qza: Protein sequences originating from requested genomes.
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68 :taxonomies.qza: Taxonomies of requested genomes.
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69
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70 |
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72 Description:
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73 ------------
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74 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.
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75
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77 |
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78
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79 </help>
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80 <citations>
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81 <citation type="doi">10.1093/nar/gkv1276</citation>
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82 <citation type="doi">10.1093/nar/gkv1189</citation>
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83 <citation type="doi">10.1093/database/baaa062</citation>
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84 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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85 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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86 </citations>
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87 </tool>