Mercurial > repos > q2d2 > qiime2__feature_table__filter_features_conditionally
view qiime2__feature_table__filter_features_conditionally.xml @ 2:78538c1b0993 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
---|---|
date | Thu, 08 Jun 2023 19:47:43 +0000 |
parents | dbeb5a365844 |
children | 09226feca49a |
line wrap: on
line source
<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2023, 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: 2023.5.0) for: qiime2 (version: 2023.5.1) --> <tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Filter features from a table based on abundance and prevalence</description> <requirements> <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table filter_features_conditionally '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which features should be filtered."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[Composition]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> <param name="abundance" type="float" min="0" max="0.999999" value="" label="abundance: Float % Range(0, 1)" help="[required] The minimum relative abundance for a feature to be retained."/> <param name="prevalence" type="float" min="0" max="0.999999" value="" label="prevalence: Float % Range(0, 1)" help="[required] The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained."/> </inputs> <outputs> <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> </outputs> <tests> <test> <param name="table" value="filter_features_conditionally.test0.feature-table.qza" ftype="qza"/> <param name="abundance" value="0.01"/> <param name="prevalence" value="0.34"/> <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-features-conditionally ==================================================== Filter features from a table based on abundance and prevalence Outputs: -------- :filtered_table.qza: The resulting feature table filtered by feature. | Description: ------------ Filter features based on the relative abundance in a certain portion of samples (i.e., features must have a relative abundance of at least `abundance` in at least `prevalence` number of samples). Any samples with a frequency of zero after feature filtering will also be removed. Examples: --------- feature_table_filter_features_conditionally ******************************************* | Retain only features with at least 1%% abundance in at least 34%% of samples. Using the ``qiime2 feature-table filter-features-conditionally`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Set *"abundance"* to ``0.01`` #. Set *"prevalence"* to ``0.34`` #. Press the ``Execute`` button. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>