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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:28:48 +0000 |
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children | 7573001162c8 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2022, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: q2galaxy (version: 2022.8.1) for: qiime2 (version: 2022.8.1) --> <tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> <description>Filter samples out of demultiplexed data.</description> <requirements> <container type="docker">quay.io/qiime2/core:2022.8</container> </requirements> <version_command>q2galaxy version demux</version_command> <command detect_errors="aggressive">q2galaxy run demux filter_samples '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required] The demultiplexed data from which samples should be filtered."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> <filter type="add_value" value="SampleData[SequencesWithQuality]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> </param> <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"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" type="select" label="metadata: Metadata"> <option value="tsv" selected="true">Metadata from TSV</option> <option value="qza">Metadata from Artifact</option> </param> <when value="tsv"> <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> </when> <when value="qza"> <param name="source" type="data" format="qza" label="Metadata Source"/> </when> </conditional> </repeat> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> <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."> <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> <option value="__q2galaxy__::control::provide">Provide a value</option> </param> <when value="__q2galaxy__::control::default"> <param name="where" type="hidden" value="__q2galaxy__::literal::None"/> </when> <when value="__q2galaxy__::control::provide"> <param name="where" type="text"> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> </when> </conditional> <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."/> </section> </inputs> <outputs> <data name="filtered_demux" format="qza" label="${tool.name} on ${on_string}: filtered_demux.qza" from_work_dir="filtered_demux.qza"/> </outputs> <tests/> <help> QIIME 2: demux filter-samples ============================= Filter samples out of demultiplexed data. Outputs: -------- :filtered_demux.qza: Filtered demultiplexed data. | Description: ------------ 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. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>