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author q2d2
date Wed, 30 Oct 2024 19:55:48 +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: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 rescript evaluate-cross-validate" id="qiime2__rescript__evaluate_cross_validate" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Evaluate DNA sequence reference database via cross-validated taxonomic classification.</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version rescript</version_command>
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22 <command detect_errors="exit_code">q2galaxy run rescript evaluate_cross_validate '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Reference sequences to use for classifier training/testing.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Sequence]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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32 </param>
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33 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomy to use for classifier training/testing.">
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34 <options options_filter_attribute="metadata.semantic_type">
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35 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
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38 </param>
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39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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40 <param name="k" type="integer" min="2" value="3" label="k: Int % Range(2, None)" help="[default: 3] Number of stratified folds."/>
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41 <param name="random_state" type="integer" min="0" value="0" label="random_state: Int % Range(0, None)" help="[default: 0] Seed used by the random number generator."/>
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42 <conditional name="__q2galaxy__GUI__conditional__reads_per_batch__">
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43 <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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44 <option value="auto" selected="true">auto (Str)</option>
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45 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option>
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46 </param>
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47 <when value="auto">
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48 <param name="reads_per_batch" type="hidden" value="auto"/>
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49 </when>
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50 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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51 <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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52 </when>
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53 </conditional>
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54 <conditional name="__q2galaxy__GUI__conditional__confidence__">
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55 <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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56 <option value="disable">disable (Str)</option>
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57 <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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58 </param>
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59 <when value="disable">
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60 <param name="confidence" type="hidden" value="disable"/>
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61 </when>
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62 <when value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)">
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63 <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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64 </when>
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65 </conditional>
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66 </section>
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67 </inputs>
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68 <outputs>
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69 <data name="expected_taxonomy" format="qza" label="${tool.name} on ${on_string}: expected_taxonomy.qza" from_work_dir="expected_taxonomy.qza"/>
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70 <data name="observed_taxonomy" format="qza" label="${tool.name} on ${on_string}: observed_taxonomy.qza" from_work_dir="observed_taxonomy.qza"/>
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71 <data name="evaluation" format="qzv" label="${tool.name} on ${on_string}: evaluation.qzv" from_work_dir="evaluation.qzv"/>
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72 </outputs>
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73 <tests/>
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74 <help>
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75 QIIME 2: rescript evaluate-cross-validate
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76 =========================================
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77 Evaluate DNA sequence reference database via cross-validated taxonomic classification.
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78
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79
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80 Outputs:
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81 --------
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82 :expected_taxonomy.qza: Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification.
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83 :observed_taxonomy.qza: Observed taxonomic label for each input sequence, predicted by cross-validation.
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84 :evaluation.qzv: Visualization of cross-validated accuracy results.
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85
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86 |
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87
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88 Description:
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89 ------------
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90 Evaluate DNA sequence reference database via cross-validated taxonomic classification. Unique taxonomic labels are truncated to enable appropriate label stratification. See the cited reference (Bokulich et al. 2018) for more details.
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91
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92
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93 |
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94
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95 </help>
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96 <citations>
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97 <citation type="doi">10.1186/s40168-018-0470-z</citation>
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98 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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99 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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100 </citations>
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101 </tool>