| Next changeset 1:7573001162c8 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__demux__filter_samples.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 4213b621e08a qiime2__demux__filter_samples.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__demux__filter_samples.xml Mon Aug 29 19:28:48 2022 +0000 |
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| @@ -0,0 +1,93 @@ +<?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> |