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annotate qiime2__feature_classifier__classify_sklearn.xml @ 0:506691306b87 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:53:31 +0000
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506691306b87 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2022, QIIME 2 development team.
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4
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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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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13 <tool name="qiime2 feature-classifier classify-sklearn" id="qiime2__feature_classifier__classify_sklearn" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Pre-fitted sklearn-based taxonomy classifier</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</container>
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17 </requirements>
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18 <version_command>q2galaxy version feature_classifier</version_command>
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19 <command detect_errors="aggressive">q2galaxy run feature_classifier classify_sklearn '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="reads" type="data" format="qza" label="reads: FeatureData[Sequence]" help="[required] The feature data to be classified.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Sequence]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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29 </param>
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30 <param name="classifier" type="data" format="qza" label="classifier: TaxonomicClassifier" help="[required] The taxonomic classifier for classifying the reads.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="TaxonomicClassifier"/>
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33 </options>
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['TaxonomicClassifier']</validator>
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35 </param>
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36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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37 <conditional name="__q2galaxy__GUI__conditional__reads_per_batch__">
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38 <param name="__q2galaxy__GUI__select__" type="select" label="reads_per_batch: Int % Range(1, None) | Str % Choices('auto')" help="[default: 'auto'] Number of reads to process in each batch. If &quot;auto&quot;, this parameter is autoscaled to min( number of query sequences / n_jobs, 20000).">
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39 <option value="auto" selected="true">auto (Str)</option>
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40 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option>
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41 </param>
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42 <when value="auto">
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43 <param name="reads_per_batch" type="hidden" value="auto"/>
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44 </when>
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45 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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46 <param name="reads_per_batch" type="integer" min="1" value="" label="reads_per_batch: Int % Range(1, None)" help="[required] Number of reads to process in each batch. If &quot;auto&quot;, this parameter is autoscaled to min( number of query sequences / n_jobs, 20000)."/>
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47 </when>
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48 </conditional>
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49 <param name="n_jobs" type="integer" value="1" label="n_jobs: Int" help="[default: 1] The maximum number of concurrently worker processes. If -1 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all CPUs but one are used."/>
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50 <param name="pre_dispatch" type="text" value="2*n_jobs" label="pre_dispatch: Str" help="[default: '2*n_jobs'] &quot;all&quot; or expression, as in &quot;3*n_jobs&quot;. The number of batches (of tasks) to be pre-dispatched.">
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51 <sanitizer>
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52 <valid initial="string.printable"/>
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53 </sanitizer>
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54 </param>
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55 <conditional name="__q2galaxy__GUI__conditional__confidence__">
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56 <param name="__q2galaxy__GUI__select__" type="select" label="confidence: Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable')" help="[default: 0.7] Confidence threshold for limiting taxonomic depth. Set to &quot;disable&quot; to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.">
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57 <option value="disable">disable (Str)</option>
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58 <option value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)" selected="true">Provide a value (Float % Range(0, 1, inclusive_end=True))</option>
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59 </param>
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60 <when value="disable">
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61 <param name="confidence" type="hidden" value="disable"/>
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62 </when>
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63 <when value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)">
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64 <param name="confidence" type="float" min="0" max="1" value="0.7" label="confidence: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.7] Confidence threshold for limiting taxonomic depth. Set to &quot;disable&quot; to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."/>
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65 </when>
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66 </conditional>
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67 <param name="read_orientation" type="select" label="read_orientation: Str % Choices('same', 'reverse-complement', 'auto')" display="radio">
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68 <option value="same">same</option>
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69 <option value="reverse-complement">reverse-complement</option>
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70 <option value="auto" selected="true">auto</option>
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71 </param>
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72 </section>
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73 </inputs>
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74 <outputs>
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75 <data name="classification" format="qza" label="${tool.name} on ${on_string}: classification.qza" from_work_dir="classification.qza"/>
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76 </outputs>
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77 <tests/>
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78 <help>
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79 QIIME 2: feature-classifier classify-sklearn
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80 ============================================
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81 Pre-fitted sklearn-based taxonomy classifier
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82
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83
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84 Outputs:
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85 --------
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86 :classification.qza: &lt;no description&gt;
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87
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88 |
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89
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90 Description:
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91 ------------
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92 Classify reads by taxon using a fitted classifier.
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93
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94
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95 |
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96
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97 </help>
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98 <citations>
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99 <citation type="bibtex">@article{cite1,
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100 author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard},
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101 journal = {Journal of machine learning research},
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102 number = {Oct},
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103 pages = {2825--2830},
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104 title = {Scikit-learn: Machine learning in Python},
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105 volume = {12},
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106 year = {2011}
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107 }
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108 </citation>
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109 <citation type="doi">10.1186/s40168-018-0470-z</citation>
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110 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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111 </citations>
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112 </tool>