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comparison qiime2__rescript__get_ncbi_genomes.xml @ 2:f8ac470cc306 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:55:35 +0000
parents 660b904210ca
children
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1:660b904210ca 2:f8ac470cc306
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2024.5.0) 9 q2galaxy (version: 2024.10.0)
10 for: 10 for:
11 qiime2 (version: 2024.5.0) 11 qiime2 (version: 2024.10.1)
12 --> 12 -->
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"> 13 <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">
14 <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description> 14 <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description>
15 <xrefs>
16 <xref type="bio.tools">qiime2</xref>
17 </xrefs>
15 <requirements> 18 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> 19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
17 </requirements> 20 </requirements>
18 <version_command>q2galaxy version rescript</version_command> 21 <version_command>q2galaxy version rescript</version_command>
19 <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command>
20 <configfiles> 23 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
26 <valid initial="string.printable"/> 29 <valid initial="string.printable"/>
27 </sanitizer> 30 </sanitizer>
28 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator> 31 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
29 </param> 32 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank')" display="radio"> 34 <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank', 'all')" display="radio">
32 <option value="refseq" selected="true">refseq</option> 35 <option value="refseq" selected="true">refseq</option>
33 <option value="genbank">genbank</option> 36 <option value="genbank">genbank</option>
37 <option value="all">all</option>
34 </param> 38 </param>
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')]"> 39 <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')]">
36 <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio"> 40 <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio">
37 <option value="__q2galaxy__::literal::None">Selection required</option> 41 <option value="__q2galaxy__::literal::None">Selection required</option>
38 <option value="complete_genome">complete_genome</option> 42 <option value="complete_genome">complete_genome</option>
41 <option value="contig">contig</option> 45 <option value="contig">contig</option>
42 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> 46 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
43 </param> 47 </param>
44 </repeat> 48 </repeat>
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."/> 49 <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."/>
50 <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)."/>
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."/> 51 <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."/>
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."/> 52 <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."/>
53 <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')]">
54 <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')">
55 <option value="__q2galaxy__::literal::None">Selection required</option>
56 <option value="domain">domain</option>
57 <option value="superkingdom">superkingdom</option>
58 <option value="kingdom">kingdom</option>
59 <option value="subkingdom">subkingdom</option>
60 <option value="superphylum">superphylum</option>
61 <option value="phylum">phylum</option>
62 <option value="subphylum">subphylum</option>
63 <option value="infraphylum">infraphylum</option>
64 <option value="superclass">superclass</option>
65 <option value="class">class</option>
66 <option value="subclass">subclass</option>
67 <option value="infraclass">infraclass</option>
68 <option value="cohort">cohort</option>
69 <option value="superorder">superorder</option>
70 <option value="order">order</option>
71 <option value="suborder">suborder</option>
72 <option value="infraorder">infraorder</option>
73 <option value="parvorder">parvorder</option>
74 <option value="superfamily">superfamily</option>
75 <option value="family">family</option>
76 <option value="subfamily">subfamily</option>
77 <option value="tribe">tribe</option>
78 <option value="subtribe">subtribe</option>
79 <option value="genus">genus</option>
80 <option value="subgenus">subgenus</option>
81 <option value="species group">species group</option>
82 <option value="species subgroup">species subgroup</option>
83 <option value="species">species</option>
84 <option value="subspecies">subspecies</option>
85 <option value="forma">forma</option>
86 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
87 </param>
88 </repeat>
89 <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'."/>
48 </section> 90 </section>
49 </inputs> 91 </inputs>
50 <outputs> 92 <outputs>
51 <data name="genome_assemblies" format="qza" label="${tool.name} on ${on_string}: genome_assemblies.qza" from_work_dir="genome_assemblies.qza"/> 93 <data name="genome_assemblies" format="qza" label="${tool.name} on ${on_string}: genome_assemblies.qza" from_work_dir="genome_assemblies.qza"/>
52 <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/> 94 <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/>