Mercurial > repos > q2d2 > qiime2__rescript__evaluate_cross_validate
comparison qiime2__rescript__evaluate_cross_validate.xml @ 0:6afd848c3650 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
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| date | Thu, 25 Apr 2024 21:20:53 +0000 |
| parents | |
| children | 3fdb4839347a |
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| 1 <?xml version='1.0' encoding='utf-8'?> | |
| 2 <!-- | |
| 3 Copyright (c) 2024, QIIME 2 development team. | |
| 4 | |
| 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
| 6 --> | |
| 7 <!-- | |
| 8 This tool was automatically generated by: | |
| 9 q2galaxy (version: 2024.2.1) | |
| 10 for: | |
| 11 qiime2 (version: 2024.2.0) | |
| 12 --> | |
| 13 <tool name="qiime2 rescript evaluate-cross-validate" id="qiime2__rescript__evaluate_cross_validate" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Evaluate DNA sequence reference database via cross-validated taxonomic classification.</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version rescript</version_command> | |
| 19 <command detect_errors="exit_code">q2galaxy run rescript evaluate_cross_validate '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="staging_path_and_source_path"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Reference sequences to use for classifier training/testing."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="FeatureData[Sequence]"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> | |
| 29 </param> | |
| 30 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomy to use for classifier training/testing."> | |
| 31 <options options_filter_attribute="metadata.semantic_type"> | |
| 32 <filter type="add_value" value="FeatureData[Taxonomy]"/> | |
| 33 </options> | |
| 34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> | |
| 35 </param> | |
| 36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 37 <param name="k" type="integer" min="2" value="3" label="k: Int % Range(2, None)" help="[default: 3] Number of stratified folds."/> | |
| 38 <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."/> | |
| 39 <conditional name="__q2galaxy__GUI__conditional__reads_per_batch__"> | |
| 40 <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 "auto", this parameter is autoscaled to min( number of query sequences / n_jobs, 20000)."> | |
| 41 <option value="auto" selected="true">auto (Str)</option> | |
| 42 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option> | |
| 43 </param> | |
| 44 <when value="auto"> | |
| 45 <param name="reads_per_batch" type="hidden" value="auto"/> | |
| 46 </when> | |
| 47 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> | |
| 48 <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 "auto", this parameter is autoscaled to min( number of query sequences / n_jobs, 20000)."/> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 <conditional name="__q2galaxy__GUI__conditional__confidence__"> | |
| 52 <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 "disable" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."> | |
| 53 <option value="disable">disable (Str)</option> | |
| 54 <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> | |
| 55 </param> | |
| 56 <when value="disable"> | |
| 57 <param name="confidence" type="hidden" value="disable"/> | |
| 58 </when> | |
| 59 <when value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)"> | |
| 60 <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 "disable" to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."/> | |
| 61 </when> | |
| 62 </conditional> | |
| 63 </section> | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 <data name="expected_taxonomy" format="qza" label="${tool.name} on ${on_string}: expected_taxonomy.qza" from_work_dir="expected_taxonomy.qza"/> | |
| 67 <data name="observed_taxonomy" format="qza" label="${tool.name} on ${on_string}: observed_taxonomy.qza" from_work_dir="observed_taxonomy.qza"/> | |
| 68 <data name="evaluation" format="qzv" label="${tool.name} on ${on_string}: evaluation.qzv" from_work_dir="evaluation.qzv"/> | |
| 69 </outputs> | |
| 70 <tests/> | |
| 71 <help> | |
| 72 QIIME 2: rescript evaluate-cross-validate | |
| 73 ========================================= | |
| 74 Evaluate DNA sequence reference database via cross-validated taxonomic classification. | |
| 75 | |
| 76 | |
| 77 Outputs: | |
| 78 -------- | |
| 79 :expected_taxonomy.qza: Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification. | |
| 80 :observed_taxonomy.qza: Observed taxonomic label for each input sequence, predicted by cross-validation. | |
| 81 :evaluation.qzv: Visualization of cross-validated accuracy results. | |
| 82 | |
| 83 | | |
| 84 | |
| 85 Description: | |
| 86 ------------ | |
| 87 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. | |
| 88 | |
| 89 | |
| 90 | | |
| 91 | |
| 92 </help> | |
| 93 <citations> | |
| 94 <citation type="doi">10.1186/s40168-018-0470-z</citation> | |
| 95 <citation type="doi">10.1371/journal.pcbi.1009581</citation> | |
| 96 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 97 </citations> | |
| 98 </tool> |