Mercurial > repos > q2d2 > qiime2__demux__filter_samples
annotate qiime2__demux__filter_samples.xml @ 1:7573001162c8 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:43:16 +0000 |
parents | 4213b621e08a |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 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__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
1
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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3 Copyright (c) 2023, QIIME 2 development team. |
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 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__demux 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__demux 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__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
1
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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9 q2galaxy (version: 2022.11.1) |
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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__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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11 qiime2 (version: 2022.11.1) |
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12 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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13 <tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2022.11.1+q2galaxy.2022.11.1.2" 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__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Filter samples out of demultiplexed data.</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/core:2022.11</container> |
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17 </requirements> |
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18 <version_command>q2galaxy version demux</version_command> |
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19 <command detect_errors="exit_code">q2galaxy run demux filter_samples '$inputs'</command> |
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20 <configfiles> |
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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__demux 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__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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24 <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required] The demultiplexed data from which samples should be filtered."> |
4213b621e08a
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 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__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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26 <filter type="add_value" value="SampleData[SequencesWithQuality]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </options> |
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30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 </param> |
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32 <repeat name="metadata" min="1" help="[required] Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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34 <param name="type" type="select" label="metadata: Metadata"> |
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35 <option value="tsv" selected="true">Metadata from TSV</option> |
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36 <option value="qza">Metadata from Artifact</option> |
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37 </param> |
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38 <when value="tsv"> |
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39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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40 </when> |
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41 <when value="qza"> |
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42 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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43 </when> |
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44 </conditional> |
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45 </repeat> |
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46 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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47 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> |
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48 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained."> |
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49 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> |
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50 <option value="__q2galaxy__::control::provide">Provide a value</option> |
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51 </param> |
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52 <when value="__q2galaxy__::control::default"> |
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53 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/> |
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54 </when> |
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55 <when value="__q2galaxy__::control::provide"> |
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56 <param name="where" type="text"> |
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57 <sanitizer> |
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58 <valid initial="string.printable"/> |
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59 </sanitizer> |
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60 </param> |
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61 </when> |
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62 </conditional> |
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63 <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data."/> |
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64 </section> |
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65 </inputs> |
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66 <outputs> |
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67 <data name="filtered_demux" format="qza" label="${tool.name} on ${on_string}: filtered_demux.qza" from_work_dir="filtered_demux.qza"/> |
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68 </outputs> |
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69 <tests/> |
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70 <help> |
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71 QIIME 2: demux filter-samples |
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72 ============================= |
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73 Filter samples out of demultiplexed data. |
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74 |
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75 |
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76 Outputs: |
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77 -------- |
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78 :filtered_demux.qza: Filtered demultiplexed data. |
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79 |
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80 | |
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81 |
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82 Description: |
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83 ------------ |
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84 Filter samples indicated in given metadata out of demultiplexed data. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified. |
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85 |
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86 |
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87 | |
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88 |
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89 </help> |
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90 <citations> |
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91 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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92 </citations> |
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93 </tool> |