| Next changeset 1:dbeb5a365844 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__feature_table__filter_features_conditionally.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 |
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| diff -r 000000000000 -r 90e36d8f2299 qiime2__feature_table__filter_features_conditionally.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__filter_features_conditionally.xml Mon Aug 29 19:56:18 2022 +0000 |
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| @@ -0,0 +1,63 @@ +<?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-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"> + <description>Filter features from a table based on abundance and prevalence</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_features_conditionally '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which features should be filtered."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Composition]"/> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> + </param> + <param name="abundance" type="float" min="0" max="0.999999" value="" label="abundance: Float % Range(0, 1)" help="[required] The minimum relative abundance for a feature to be retained."/> + <param name="prevalence" type="float" min="0" max="0.999999" value="" label="prevalence: Float % Range(0, 1)" help="[required] The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained."/> + </inputs> + <outputs> + <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> + </outputs> + <tests/> + <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. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> |
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