Mercurial > repos > q2d2 > qiime2__feature_table__filter_seqs
changeset 0:34b8ff5edea8 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 19:59:11 +0000 |
| parents | |
| children | e7b65e8f7e68 |
| files | qiime2__feature_table__filter_seqs.xml test-data/merge.test0.feature-table1.qza test-data/merge.test0.feature-table2.qza test-data/merge.test1.feature-table1.qza test-data/merge.test1.feature-table2.qza test-data/merge.test1.feature-table3.qza |
| diffstat | 6 files changed, 98 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__filter_seqs.xml Mon Aug 29 19:59:11 2022 +0000 @@ -0,0 +1,98 @@ +<?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 feature-table filter-seqs" id="qiime2__feature_table__filter_seqs" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Filter features from sequences</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version feature_table</version_command> + <command detect_errors="aggressive">q2galaxy run feature_table filter_seqs '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </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>