Mercurial > repos > q2d2 > qiime2__taxa__filter_table
annotate qiime2__taxa__filter_table.xml @ 4:a8972ecf15c1 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:32:22 +0000 |
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6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
3
e4872ac2c683
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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3 Copyright (c) 2024, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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a8972ecf15c1
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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9 q2galaxy (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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11 qiime2 (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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a8972ecf15c1
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 taxa filter-table" id="qiime2__taxa__filter_table" version="2024.5.0+q2galaxy.2024.5.0" 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Taxonomy-based feature table filter.</description> |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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a8972ecf15c1
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version taxa</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run taxa filter_table '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | PresenceAbsence²]" help="[required] Feature table to be filtered."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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a8972ecf15c1
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit c7e80dcda727ce63b42aa8a946e9330310929797
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 </param> |
6dddc1627343
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 <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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <conditional name="__q2galaxy__GUI__conditional__include__" label="include: Str"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 <param name="__q2galaxy__GUI__select__" type="select" label="include: Str" help="[optional] One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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40 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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42 </param> |
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43 <when value="__q2galaxy__::control::default"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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44 <param name="include" type="hidden" value="__q2galaxy__::literal::None"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 <when value="__q2galaxy__::control::provide"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 <param name="include" type="text"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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48 <sanitizer> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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49 <valid initial="string.printable"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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50 </sanitizer> |
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51 </param> |
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52 </when> |
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53 </conditional> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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54 <conditional name="__q2galaxy__GUI__conditional__exclude__" label="exclude: Str"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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55 <param name="__q2galaxy__GUI__select__" type="select" label="exclude: Str" help="[optional] One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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56 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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57 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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58 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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59 <when value="__q2galaxy__::control::default"> |
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60 <param name="exclude" type="hidden" value="__q2galaxy__::literal::None"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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61 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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62 <when value="__q2galaxy__::control::provide"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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63 <param name="exclude" type="text"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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64 <sanitizer> |
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65 <valid initial="string.printable"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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66 </sanitizer> |
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67 </param> |
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68 </when> |
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69 </conditional> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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70 <param name="query_delimiter" type="text" value="," label="query_delimiter: Str" help="[default: ','] The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations."> |
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71 <sanitizer> |
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72 <valid initial="string.printable"/> |
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73 </sanitizer> |
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74 </param> |
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75 <param name="mode" type="select" label="mode: Str % Choices('exact', 'contains')" display="radio"> |
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76 <option value="exact">exact</option> |
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77 <option value="contains" selected="true">contains</option> |
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78 </param> |
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79 </section> |
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80 </inputs> |
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81 <outputs> |
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82 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> |
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83 </outputs> |
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84 <tests/> |
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85 <help> |
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86 QIIME 2: taxa filter-table |
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87 ========================== |
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88 Taxonomy-based feature table filter. |
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89 |
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90 |
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91 Outputs: |
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92 -------- |
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93 :filtered_table.qza: The taxonomy-filtered feature table. |
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94 |
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95 | |
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96 |
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97 Description: |
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98 ------------ |
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99 This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table. |
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100 |
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101 |
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102 | |
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103 |
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104 </help> |
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105 <citations> |
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106 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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107 </citations> |
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108 </tool> |