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date Thu, 25 Apr 2024 21:24:14 +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: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 rescript evaluate-classifications" id="qiime2__rescript__evaluate_classifications" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Interactively evaluate taxonomic classification accuracy.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</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 evaluate_classifications '$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 <param name="expected_taxonomies" type="data" format="qza" label="expected_taxonomies: List[FeatureData[Taxonomy]]" help="[required] True taxonomic labels for one more more sets of features." multiple="true">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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27 </options>
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28 </param>
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29 <param name="observed_taxonomies" type="data" format="qza" label="observed_taxonomies: List[FeatureData[Taxonomy]]" help="[required] Predicted classifications of same sets of features, input in same order as expected_taxonomies." multiple="true">
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30 <options options_filter_attribute="metadata.semantic_type">
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31 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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32 </options>
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33 </param>
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34 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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35 <repeat name="labels" help="[optional] List of labels to use for labeling evaluation results in the resulting visualization. Inputs are labeled with labels in the order that each is input. If there are fewer labels than inputs (or no labels), unnamed inputs are labeled numerically in sequential order. Extra labels are ignored." title="labels: List[Str]">
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36 <param name="element" type="text" label="element: Str" help="[required]">
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37 <sanitizer>
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38 <valid initial="string.printable"/>
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39 </sanitizer>
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40 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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41 </param>
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42 </repeat>
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43 </section>
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44 </inputs>
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45 <outputs>
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46 <data name="evaluation" format="qzv" label="${tool.name} on ${on_string}: evaluation.qzv" from_work_dir="evaluation.qzv"/>
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47 </outputs>
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48 <tests/>
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49 <help>
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50 QIIME 2: rescript evaluate-classifications
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51 ==========================================
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52 Interactively evaluate taxonomic classification accuracy.
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53
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54
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55 Outputs:
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56 --------
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57 :evaluation.qzv: Visualization of classification accuracy results.
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58
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59 |
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60
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61 Description:
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62 ------------
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63 Evaluate taxonomic classification accuracy by comparing one or more sets of true taxonomic labels to the predicted taxonomies for the same set(s) of features. Output an interactive line plot of classification accuracy for each pair of expected/observed taxonomies. The x-axis in these plots represents the taxonomic levels present in the input taxonomies so are labeled numerically instead of by rank, but typically for 7-level taxonomies these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class, 4 = order, 5 = family, 6 = genus, 7 = species.
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64
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65
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66 |
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67
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68 </help>
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69 <citations>
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70 <citation type="doi">10.1186/s40168-018-0470-z</citation>
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71 <citation type="doi">10.1128/mSystems.00219-18</citation>
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72 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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73 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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74 </citations>
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75 </tool>