Mercurial > repos > q2d2 > qiime2__feature_table__filter_features_conditionally
diff qiime2__feature_table__filter_features_conditionally.xml @ 1:dbeb5a365844 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:52:51 +0000 |
parents | 90e36d8f2299 |
children | 78538c1b0993 |
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--- a/qiime2__feature_table__filter_features_conditionally.xml Mon Aug 29 19:56:18 2022 +0000 +++ b/qiime2__feature_table__filter_features_conditionally.xml Fri Jan 13 22:52:51 2023 +0000 @@ -1,32 +1,32 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +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: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2022.11.1+q2galaxy.2022.11.1.2" 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:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version feature_table</version_command> - <command detect_errors="aggressive">q2galaxy run feature_table filter_features_conditionally '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run feature_table filter_features_conditionally '$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[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[Composition]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> - <filter type="add_value" value="FeatureTable[Frequency]"/> - <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> @@ -36,7 +36,20 @@ <outputs> <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> </outputs> - <tests/> + <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 ==================================================== @@ -53,6 +66,19 @@ ------------ 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. + + |