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author | q2d2 |
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date | Mon, 03 Jun 2024 23:27:00 +0000 |
parents | 4e61dddfe0b5 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2024, 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: 2024.5.0) for: qiime2 (version: 2024.5.0) --> <tool name="qiime2 feature-table filter-seqs" id="qiime2__feature_table__filter_seqs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Filter features from sequences</description> <requirements> <container type="docker">quay.io/qiime2/amplicon:2024.5</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table filter_seqs '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="data" type="data" format="qza" label="data: FeatureData[Sequence¹ | AlignedSequence²]" help="[required] The sequences from which features should be filtered."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureData[Sequence]"/> <filter type="add_value" value="FeatureData[AlignedSequence]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[Frequency]" help="[optional] Table containing feature ids used for id-based filtering."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> </param> <repeat name="metadata" help="[optional] Feature metadata used for id-based filtering, with `where` parameter when selecting features to retain, or with `exclude_ids` when selecting features to discard." 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> <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the sequences 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] If true, the features selected by the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences instead of being retained."/> </section> </inputs> <outputs> <data name="filtered_data" format="qza" label="${tool.name} on ${on_string}: filtered_data.qza" from_work_dir="filtered_data.qza"/> </outputs> <tests/> <help> QIIME 2: feature-table filter-seqs ================================== Filter features from sequences Outputs: -------- :filtered_data.qza: The resulting filtered sequences. | Description: ------------ Filter features from sequences based on a feature table or metadata. See the filtering tutorial on https://docs.qiime2.org for additional details. This method can filter based on ids in a table or a metadata file, but not both (i.e., the table and metadata options are mutually exclusive). | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>