Mercurial > repos > q2d2 > qiime2__quality_control__evaluate_taxonomy
annotate qiime2__quality_control__evaluate_taxonomy.xml @ 2:13f0559220c2 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
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date | Thu, 08 Jun 2023 19:51:07 +0000 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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2719c0bf3bd7
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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3 Copyright (c) 2023, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
e0a2f5dead31
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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9 q2galaxy (version: 2023.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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13f0559220c2
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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11 qiime2 (version: 2023.5.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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13f0559220c2
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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13 <tool name="qiime2 quality-control evaluate-taxonomy" id="qiime2__quality_control__evaluate_taxonomy" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Evaluate expected vs. observed taxonomic assignments</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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13f0559220c2
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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16 <container type="docker">quay.io/qiime2/core:2023.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version quality_control</version_command> |
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2719c0bf3bd7
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run quality_control evaluate_taxonomy '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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21 <inputs name="inputs" data_style="paths"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="expected_taxa" type="data" format="qza" label="expected_taxa: FeatureData[Taxonomy]" help="[required] Expected taxonomic assignments"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureData[Taxonomy]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 </options> |
e0a2f5dead31
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 <param name="observed_taxa" type="data" format="qza" label="observed_taxa: FeatureData[Taxonomy]" help="[required] Observed taxonomic assignments"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <filter type="add_value" value="FeatureData[Taxonomy]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <param name="depth" type="integer" value="" label="depth: Int" help="[required] Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database)."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <param name="feature_table" type="data" format="qza" optional="true" label="feature_table: FeatureTable[RelativeFrequency]" help="[optional] Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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40 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 </options> |
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42 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator> |
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43 </param> |
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44 <param name="palette" type="select" label="palette: Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow')"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 <option value="Set1" selected="true">Set1</option> |
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46 <option value="Set2">Set2</option> |
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47 <option value="Set3">Set3</option> |
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48 <option value="Pastel1">Pastel1</option> |
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49 <option value="Pastel2">Pastel2</option> |
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50 <option value="Paired">Paired</option> |
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51 <option value="Accent">Accent</option> |
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52 <option value="Dark2">Dark2</option> |
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53 <option value="tab10">tab10</option> |
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54 <option value="tab20">tab20</option> |
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55 <option value="tab20b">tab20b</option> |
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56 <option value="tab20c">tab20c</option> |
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57 <option value="viridis">viridis</option> |
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58 <option value="plasma">plasma</option> |
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59 <option value="inferno">inferno</option> |
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60 <option value="magma">magma</option> |
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61 <option value="terrain">terrain</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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62 <option value="rainbow">rainbow</option> |
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63 </param> |
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64 <param name="require_exp_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="require_exp_ids: Bool" help="[default: Yes] Require that all features found in observed taxa must be found in expected taxa or raise error."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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65 <param name="require_obs_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="require_obs_ids: Bool" help="[default: Yes] Require that all features found in expected taxa must be found in observed taxa or raise error."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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66 <conditional name="__q2galaxy__GUI__conditional__sample_id__" label="sample_id: Str"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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67 <param name="__q2galaxy__GUI__select__" type="select" label="sample_id: Str" help="[optional] Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample_id is provided, feature frequencies are derived from the sum of all samples present in the feature table."> |
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68 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> |
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69 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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70 </param> |
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71 <when value="__q2galaxy__::control::default"> |
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72 <param name="sample_id" type="hidden" value="__q2galaxy__::literal::None"/> |
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73 </when> |
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74 <when value="__q2galaxy__::control::provide"> |
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75 <param name="sample_id" type="text"> |
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76 <sanitizer> |
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77 <valid initial="string.printable"/> |
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78 </sanitizer> |
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79 </param> |
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80 </when> |
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81 </conditional> |
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82 </section> |
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83 </inputs> |
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84 <outputs> |
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85 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> |
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86 </outputs> |
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87 <tests/> |
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88 <help> |
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89 QIIME 2: quality-control evaluate-taxonomy |
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90 ========================================== |
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91 Evaluate expected vs. observed taxonomic assignments |
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92 |
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93 |
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94 Outputs: |
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95 -------- |
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96 :visualization.qzv: <no description> |
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97 |
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98 | |
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99 |
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100 Description: |
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101 ------------ |
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102 This visualizer compares a pair of observed and expected taxonomic assignments to calculate precision, recall, and F-measure at each taxonomic level, up to maximum level specified by the depth parameter. These metrics are calculated at each semicolon-delimited rank. This action is useful for comparing the accuracy of taxonomic assignment, e.g., between different taxonomy classifiers or other bioinformatics methods. Expected taxonomies should be derived from simulated or mock community sequences that have known taxonomic affiliations. |
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103 |
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104 |
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105 | |
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106 |
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107 </help> |
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108 <citations> |
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109 <citation type="bibtex">@article{cite1, |
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110 author = {Bokulich, Nicholas A and Kaehler, Benjamin D and Rideout, Jai Ram and Dillon, Matthew and Bolyen, Evan and Knight, Rob and Huttley, Gavin A and Caporaso, J Gregory}, |
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111 journal = {Microbiome}, |
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112 title = {Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin}, |
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113 volume = {In Press}, |
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114 year = {2018} |
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115 } |
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116 </citation> |
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117 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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118 </citations> |
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119 </tool> |