Mercurial > repos > q2d2 > qiime2__diversity__filter_distance_matrix
comparison qiime2__diversity__filter_distance_matrix.xml @ 0:3e9db2758fd2 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
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| date | Mon, 29 Aug 2022 19:38:17 +0000 |
| parents | |
| children | 40dc453ee8fd |
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| -1:000000000000 | 0:3e9db2758fd2 |
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| 1 <?xml version='1.0' encoding='utf-8'?> | |
| 2 <!-- | |
| 3 Copyright (c) 2022, QIIME 2 development team. | |
| 4 | |
| 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
| 6 --> | |
| 7 <!-- | |
| 8 This tool was automatically generated by: | |
| 9 q2galaxy (version: 2022.8.1) | |
| 10 for: | |
| 11 qiime2 (version: 2022.8.1) | |
| 12 --> | |
| 13 <tool name="qiime2 diversity filter-distance-matrix" id="qiime2__diversity__filter_distance_matrix" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Filter samples from a distance matrix.</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version diversity</version_command> | |
| 19 <command detect_errors="aggressive">q2galaxy run diversity filter_distance_matrix '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="paths"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] Distance matrix to filter by sample."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="DistanceMatrix"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator> | |
| 29 </param> | |
| 30 <repeat name="metadata" min="1" help="[required] Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude_ids` when selecting samples to discard." title="metadata: Metadata"> | |
| 31 <conditional name="__q2galaxy__GUI__conditional__metadata__"> | |
| 32 <param name="type" type="select" label="metadata: Metadata"> | |
| 33 <option value="tsv" selected="true">Metadata from TSV</option> | |
| 34 <option value="qza">Metadata from Artifact</option> | |
| 35 </param> | |
| 36 <when value="tsv"> | |
| 37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> | |
| 38 </when> | |
| 39 <when value="qza"> | |
| 40 <param name="source" type="data" format="qza" label="Metadata Source"/> | |
| 41 </when> | |
| 42 </conditional> | |
| 43 </repeat> | |
| 44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 45 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> | |
| 46 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained."> | |
| 47 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> | |
| 48 <option value="__q2galaxy__::control::provide">Provide a value</option> | |
| 49 </param> | |
| 50 <when value="__q2galaxy__::control::default"> | |
| 51 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/> | |
| 52 </when> | |
| 53 <when value="__q2galaxy__::control::provide"> | |
| 54 <param name="where" type="text"> | |
| 55 <sanitizer> | |
| 56 <valid initial="string.printable"/> | |
| 57 </sanitizer> | |
| 58 </param> | |
| 59 </when> | |
| 60 </conditional> | |
| 61 <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained."/> | |
| 62 </section> | |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data name="filtered_distance_matrix" format="qza" label="${tool.name} on ${on_string}: filtered_distance_matrix.qza" from_work_dir="filtered_distance_matrix.qza"/> | |
| 66 </outputs> | |
| 67 <tests/> | |
| 68 <help> | |
| 69 QIIME 2: diversity filter-distance-matrix | |
| 70 ========================================= | |
| 71 Filter samples from a distance matrix. | |
| 72 | |
| 73 | |
| 74 Outputs: | |
| 75 -------- | |
| 76 :filtered_distance_matrix.qza: Distance matrix filtered to include samples matching search criteria | |
| 77 | |
| 78 | | |
| 79 | |
| 80 Description: | |
| 81 ------------ | |
| 82 Filter samples from a distance matrix, retaining only the samples matching search criteria specified by `metadata` and `where` parameters (or retaining only the samples not matching that criteria, if `exclude_ids` is True). See the filtering tutorial on https://docs.qiime2.org for additional details. | |
| 83 | |
| 84 | |
| 85 | | |
| 86 | |
| 87 </help> | |
| 88 <citations> | |
| 89 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 90 </citations> | |
| 91 </tool> |