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author | q2d2 |
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date | Mon, 03 Jun 2024 23:24:54 +0000 |
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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-samples" id="qiime2__feature_table__filter_samples" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Filter samples from table</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_samples '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which samples should be filtered."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Composition]"/> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="min_frequency" type="integer" value="0" label="min_frequency: Int" help="[default: 0] The minimum total frequency that a sample must have to be retained."/> <param name="max_frequency" type="integer" optional="true" label="max_frequency: Int" help="[optional] The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied)."/> <param name="min_features" type="integer" value="0" label="min_features: Int" help="[default: 0] The minimum number of features that a sample must have to be retained."/> <param name="max_features" type="integer" optional="true" label="max_features: Int" help="[optional] The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied)."/> <repeat name="metadata" help="[optional] Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude_ids` when selecting samples 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 sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table 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 samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained."/> <param name="filter_empty_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="filter_empty_features: Bool" help="[default: Yes] If true, features which are not present in any retained samples are dropped."/> <param name="allow_empty_table" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_empty_table: Bool" help="[default: No] If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty."/> </section> </inputs> <outputs> <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> </outputs> <tests> <test> <param name="table" value="filter_samples.test0.feature-table.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="filter_samples.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test1.feature-table.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="filter_samples.test1.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <param name="where" value="__ob__body-site__cb__ IN (__dq__left palm__dq____comma__ __dq__right palm__dq__)"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test2.feature-table.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="filter_samples.test2.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND __ob__body-site__cb__=__dq__gut__dq__"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test3.feature-table.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="filter_samples.test3.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <param name="where" value="__ob__body-site__cb__=__dq__gut__dq__ OR __ob__reported-antibiotic-usage__cb__=__dq__Yes__dq__"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test4.feature-table.qza" ftype="qza"/> <repeat name="metadata"> <conditional name="__q2galaxy__GUI__conditional__metadata__"> <param name="type" value="tsv"/> <param name="source" value="filter_samples.test4.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND NOT __ob__body-site__cb__=__dq__gut__dq__"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test5.feature-table.qza" ftype="qza"/> <param name="min_features" value="10"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> <test> <param name="table" value="filter_samples.test6.feature-table.qza" ftype="qza"/> <param name="min_frequency" value="1500"/> <output name="filtered_table" ftype="qza"> <assert_contents> <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> <has_line_matching expression="type: FeatureTable\[Frequency\]"/> </has_archive_member> </assert_contents> </output> </test> </tests> <help> QIIME 2: feature-table filter-samples ===================================== Filter samples from table Outputs: -------- :filtered_table.qza: The resulting feature table filtered by sample. | Description: ------------ Filter samples from table based on frequency and/or metadata. Any features with a frequency of zero after sample filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details. Examples: --------- filter_to_subject1 ****************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section #. For *"metadata"*: - Press the ``+ Insert metadata`` button to set up the next steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``sample-metadata.tsv`` #. Set *"where"* to ``[subject]="subject-1"`` #. Press the ``Execute`` button. filter_to_skin ************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section #. For *"metadata"*: - Press the ``+ Insert metadata`` button to set up the next steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``sample-metadata.tsv`` #. Set *"where"* to ``[body-site] IN ("left palm", "right palm")`` #. Press the ``Execute`` button. filter_to_subject1_gut ********************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section #. For *"metadata"*: - Press the ``+ Insert metadata`` button to set up the next steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``sample-metadata.tsv`` #. Set *"where"* to ``[subject]="subject-1" AND [body-site]="gut"`` #. Press the ``Execute`` button. filter_to_gut_or_abx ******************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section #. For *"metadata"*: - Press the ``+ Insert metadata`` button to set up the next steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``sample-metadata.tsv`` #. Set *"where"* to ``[body-site]="gut" OR [reported-antibiotic-usage]="Yes"`` #. Press the ``Execute`` button. filter_to_subject1_not_gut ************************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section #. For *"metadata"*: - Press the ``+ Insert metadata`` button to set up the next steps. #. Leave as ``Metadata from TSV`` #. Set *"Metadata Source"* to ``sample-metadata.tsv`` #. Set *"where"* to ``[subject]="subject-1" AND NOT [body-site]="gut"`` #. Press the ``Execute`` button. filter_min_features ******************* Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section - Set *"min_features"* to ``10`` #. Press the ``Execute`` button. filter_min_frequency ******************** Using the ``qiime2 feature-table filter-samples`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section - Set *"min_frequency"* to ``1500`` #. Press the ``Execute`` button. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>