Mercurial > repos > q2d2 > qiime2__taxa__filter_seqs
annotate qiime2__taxa__filter_seqs.xml @ 2:2e3425c03486 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
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date | Thu, 08 Jun 2023 19:52:48 +0000 |
parents | c4e992863672 |
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5aedcbff85e4
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'?> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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c4e992863672
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
5aedcbff85e4
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) |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
5aedcbff85e4
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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2e3425c03486
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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2e3425c03486
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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2e3425c03486
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 65e4952f33eb335528e8553150e9097e5ea8f556
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13 <tool name="qiime2 taxa filter-seqs" id="qiime2__taxa__filter_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> |
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5aedcbff85e4
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 sequence filter.</description> |
5aedcbff85e4
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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2e3425c03486
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__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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c4e992863672
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_seqs '$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 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
5aedcbff85e4
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 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Feature sequences to be filtered."> |
5aedcbff85e4
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"> |
5aedcbff85e4
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="FeatureData[Sequence]"/> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 </options> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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[Sequence]']</validator> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </param> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored."> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 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__taxa 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__taxa 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__taxa 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__taxa 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__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <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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37 <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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38 <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 sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included."> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 <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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40 <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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41 </param> |
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42 <when value="__q2galaxy__::control::default"> |
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43 <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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44 </when> |
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45 <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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46 <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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47 <sanitizer> |
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48 <valid initial="string.printable"/> |
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49 </sanitizer> |
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50 </param> |
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51 </when> |
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52 </conditional> |
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53 <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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54 <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 sequences. 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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55 <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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56 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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57 </param> |
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58 <when value="__q2galaxy__::control::default"> |
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59 <param name="exclude" type="hidden" value="__q2galaxy__::literal::None"/> |
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60 </when> |
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61 <when value="__q2galaxy__::control::provide"> |
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62 <param name="exclude" type="text"> |
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63 <sanitizer> |
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64 <valid initial="string.printable"/> |
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65 </sanitizer> |
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66 </param> |
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67 </when> |
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68 </conditional> |
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69 <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."> |
5aedcbff85e4
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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70 <sanitizer> |
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71 <valid initial="string.printable"/> |
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72 </sanitizer> |
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73 </param> |
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74 <param name="mode" type="select" label="mode: Str % Choices('exact', 'contains')" display="radio"> |
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75 <option value="exact">exact</option> |
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76 <option value="contains" selected="true">contains</option> |
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77 </param> |
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78 </section> |
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79 </inputs> |
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80 <outputs> |
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81 <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/> |
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82 </outputs> |
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83 <tests/> |
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84 <help> |
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85 QIIME 2: taxa filter-seqs |
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86 ========================= |
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87 Taxonomy-based feature sequence filter. |
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88 |
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89 |
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90 Outputs: |
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91 -------- |
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92 :filtered_sequences.qza: The taxonomy-filtered feature sequences. |
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93 |
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94 | |
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95 |
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96 Description: |
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97 ------------ |
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98 This method filters sequences based on their taxonomic annotations. Features can be retained in the result by specifying one or more include search terms, and can be filtered out of the result 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. |
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99 |
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100 |
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101 | |
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102 |
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103 </help> |
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104 <citations> |
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105 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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106 </citations> |
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107 </tool> |