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annotate qiime2__rescript__get_silva_data.xml @ 1:e46b70a4eccd draft

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author q2d2
date Mon, 03 Jun 2024 23:30:52 +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:
1
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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-silva-data" id="qiime2__rescript__get_silva_data" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Download, parse, and import SILVA database.</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_silva_data '$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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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25 <param name="version" type="select" label="version: Str % Choices('128', '132')¹ | Str % Choices('138')² | Str % Choices('138.1')³" help="[default: '138.1'] SILVA database version to download.">
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26 <option value="128">128 (Str)</option>
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27 <option value="132">132 (Str)</option>
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28 <option value="138">138 (Str)</option>
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29 <option value="138.1" selected="true">138.1 (Str)</option>
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30 </param>
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31 <param name="target" type="select" label="target: Str % Choices('SSURef_NR99', 'SSURef', 'LSURef')¹ | Str % Choices('SSURef_NR99', 'SSURef')² | Str % Choices('SSURef_NR99', 'SSURef', 'LSURef_NR99', 'LSURef')³" help="[default: 'SSURef_NR99'] Reference sequence target to download. SSURef = redundant small subunit reference. LSURef = redundant large subunit reference. SSURef_NR99 = non-redundant (clustered at 99% similarity) small subunit reference.">
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32 <option value="SSURef_NR99" selected="true">SSURef_NR99 (Str)</option>
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33 <option value="SSURef">SSURef (Str)</option>
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34 <option value="LSURef">LSURef (Str)</option>
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35 <option value="LSURef_NR99">LSURef_NR99 (Str)</option>
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36 </param>
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37 <param name="include_species_labels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="include_species_labels: Bool" help="[default: No] Include species rank labels in taxonomy output. Note: species-labels may not be reliable in all cases."/>
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38 <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'."/>
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39 <repeat name="ranks" help="[optional] List of taxonomic ranks for building a taxonomy from the SILVA Taxonomy database. Use 'include_species_labels' to append the organism name as the species label. [default: 'domain', 'phylum', 'class', 'order', 'family', 'genus']" title="ranks: List[Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus')]">
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40 <param name="element" type="select" label="element: Str % Choices('domain', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus')">
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41 <option value="__q2galaxy__::literal::None">Selection required</option>
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42 <option value="domain">domain</option>
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43 <option value="superkingdom">superkingdom</option>
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44 <option value="kingdom">kingdom</option>
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45 <option value="subkingdom">subkingdom</option>
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46 <option value="superphylum">superphylum</option>
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47 <option value="phylum">phylum</option>
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48 <option value="subphylum">subphylum</option>
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49 <option value="infraphylum">infraphylum</option>
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50 <option value="superclass">superclass</option>
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51 <option value="class">class</option>
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52 <option value="subclass">subclass</option>
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53 <option value="infraclass">infraclass</option>
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54 <option value="superorder">superorder</option>
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55 <option value="order">order</option>
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56 <option value="suborder">suborder</option>
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57 <option value="superfamily">superfamily</option>
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58 <option value="family">family</option>
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59 <option value="subfamily">subfamily</option>
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60 <option value="genus">genus</option>
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61 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
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62 </param>
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63 </repeat>
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64 <param name="download_sequences" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="download_sequences: Bool" help="[default: Yes] Toggle whether or not to download and import the SILVA reference sequences associated with the release. Skipping the sequences is useful if you only want to download and parse the taxonomy, e.g., a local copy of the sequences already exists or for testing purposes. NOTE: if this option is used, a `silva_sequences` output is still created, but contains no data."/>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="silva_sequences" format="qza" label="${tool.name} on ${on_string}: silva_sequences.qza" from_work_dir="silva_sequences.qza"/>
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69 <data name="silva_taxonomy" format="qza" label="${tool.name} on ${on_string}: silva_taxonomy.qza" from_work_dir="silva_taxonomy.qza"/>
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70 </outputs>
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71 <tests/>
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72 <help>
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73 QIIME 2: rescript get-silva-data
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74 ================================
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75 Download, parse, and import SILVA database.
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76
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77
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78 Outputs:
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79 --------
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80 :silva_sequences.qza: SILVA reference sequences.
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81 :silva_taxonomy.qza: SILVA reference taxonomy.
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82
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83 |
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84
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85 Description:
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86 ------------
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87 Download, parse, and import SILVA database files, given a version number and reference target. Downloads data directly from SILVA, parses the taxonomy files, and outputs ready-to-use sequence and taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. NOTE: THIS ACTION ACQUIRES DATA FROM THE SILVA DATABASE. SEE https://www.arb-silva.de/silva-license-information/ FOR MORE INFORMATION and be aware that earlier versions may be released under a different license.
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88
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89
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90 |
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91
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92 </help>
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93 <citations>
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94 <citation type="bibtex">@article{cite1,
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95 author = {Pruesse, Elmar and Quast, Christian and Knittel, Katrin and Fuchs, Bernhard M and Ludwig, Wolfgang and Peplies, Jorg and Glockner, Frank Oliver},
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96 journal = {Nucleic Acids Res},
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97 number = {21},
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98 pages = {7188-7196},
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99 title = {SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB},
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100 volume = {35},
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101 year = {2007}
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102 }
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103 </citation>
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104 <citation type="bibtex">@article{cite2,
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105 author = {Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken, Jan and Schweer, Timmy and Yarza, Pablo and Peplies, Jorg and Glockner, Frank Oliver},
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106 journal = {Nucleic Acids Res},
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107 number = {Database issue},
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108 pages = {D590-6},
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109 publisher = {Oxford University Press},
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110 title = {The SILVA ribosomal RNA gene database project: improved data processing and web-based tools},
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111 volume = {41},
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112 year = {2013}
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113 }
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114 </citation>
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115 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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116 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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117 </citations>
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118 </tool>