Mercurial > repos > q2d2 > qiime2__rescript__get_ncbi_genomes

annotate qiime2__rescript__get_ncbi_genomes.xml @ 2:f8ac470cc306 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
2 <!--
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
3 Copyright (c) 2024, QIIME 2 development team.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
4
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
6 -->
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
7 <!--
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
9 q2galaxy (version: 2024.10.0)
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
10 for:
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
11 qiime2 (version: 2024.10.1)
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
12 -->
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
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">
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
14 <description>Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.</description>
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
15 <xrefs>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
16 <xref type="bio.tools">qiime2</xref>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
17 </xrefs>
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
18 <requirements>
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
20 </requirements>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
21 <version_command>q2galaxy version rescript</version_command>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
22 <command detect_errors="exit_code">q2galaxy run rescript get_ncbi_genomes '$inputs'</command>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
23 <configfiles>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
25 </configfiles>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
26 <inputs>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
27 <param name="taxon" type="text" label="taxon: Str" help="[required] NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.">
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
28 <sanitizer>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
29 <valid initial="string.printable"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
30 </sanitizer>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
31 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
32 </param>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
34 <param name="assembly_source" type="select" label="assembly_source: Str % Choices('refseq', 'genbank', 'all')" display="radio">
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
35 <option value="refseq" selected="true">refseq</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
36 <option value="genbank">genbank</option>
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
37 <option value="all">all</option>
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
38 </param>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
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')]">
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
40 <param name="element" type="select" label="element: Str % Choices('complete_genome', 'chromosome', 'scaffold', 'contig')" display="radio">
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
41 <option value="__q2galaxy__::literal::None">Selection required</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
42 <option value="complete_genome">complete_genome</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
43 <option value="chromosome">chromosome</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
44 <option value="scaffold">scaffold</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
45 <option value="contig">contig</option>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
46 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
47 </param>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
48 </repeat>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
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."/>
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
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)."/>
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
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."/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
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."/>
2
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
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')]">
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
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')">
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
55 <option value="__q2galaxy__::literal::None">Selection required</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
56 <option value="domain">domain</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
57 <option value="superkingdom">superkingdom</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
58 <option value="kingdom">kingdom</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
59 <option value="subkingdom">subkingdom</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
60 <option value="superphylum">superphylum</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
61 <option value="phylum">phylum</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
62 <option value="subphylum">subphylum</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
63 <option value="infraphylum">infraphylum</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
64 <option value="superclass">superclass</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
65 <option value="class">class</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
66 <option value="subclass">subclass</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
67 <option value="infraclass">infraclass</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
68 <option value="cohort">cohort</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
69 <option value="superorder">superorder</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
70 <option value="order">order</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
71 <option value="suborder">suborder</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
72 <option value="infraorder">infraorder</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
73 <option value="parvorder">parvorder</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
74 <option value="superfamily">superfamily</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
75 <option value="family">family</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
76 <option value="subfamily">subfamily</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
77 <option value="tribe">tribe</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
78 <option value="subtribe">subtribe</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
79 <option value="genus">genus</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
80 <option value="subgenus">subgenus</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
81 <option value="species group">species group</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
82 <option value="species subgroup">species subgroup</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
83 <option value="species">species</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
84 <option value="subspecies">subspecies</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
85 <option value="forma">forma</option>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
86 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
87 </param>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
88 </repeat>
f8ac470cc306 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
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'."/>
0
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
90 </section>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
91 </inputs>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
92 <outputs>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
93 <data name="genome_assemblies" format="qza" label="${tool.name} on ${on_string}: genome_assemblies.qza" from_work_dir="genome_assemblies.qza"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
94 <data name="loci" format="qza" label="${tool.name} on ${on_string}: loci.qza" from_work_dir="loci.qza"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
95 <data name="proteins" format="qza" label="${tool.name} on ${on_string}: proteins.qza" from_work_dir="proteins.qza"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
96 <data name="taxonomies" format="qza" label="${tool.name} on ${on_string}: taxonomies.qza" from_work_dir="taxonomies.qza"/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
97 </outputs>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
98 <tests/>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
99 <help>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
100 QIIME 2: rescript get-ncbi-genomes
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
101 ==================================
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
102 Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
103
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
104
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
105 Outputs:
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
106 --------
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
107 :genome_assemblies.qza: Nucleotide sequences of requested genomes.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
108 :loci.qza: Loci features of requested genomes.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
109 :proteins.qza: Protein sequences originating from requested genomes.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
110 :taxonomies.qza: Taxonomies of requested genomes.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
111
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
112 |
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
113
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
114 Description:
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
115 ------------
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
116 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.
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
117
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
118
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
119 |
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
120
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
121 </help>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
122 <citations>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
123 <citation type="doi">10.1093/nar/gkv1276</citation>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
124 <citation type="doi">10.1093/nar/gkv1189</citation>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
125 <citation type="doi">10.1093/database/baaa062</citation>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
126 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
127 <citation type="doi">10.1038/s41587-019-0209-9</citation>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
128 </citations>
daf0663a0679 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
129 </tool>