Mercurial > repos > q2d2 > qiime2__feature_table__filter_samples
changeset 0:e2b704eca815 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 19:55:05 +0000 |
| parents | |
| children | 552388e54b68 |
| files | qiime2__feature_table__filter_samples.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 |
| diffstat | 6 files changed, 99 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__filter_samples.xml Mon Aug 29 19:55:05 2022 +0000 @@ -0,0 +1,99 @@ +<?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-samples" id="qiime2__feature_table__filter_samples" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Filter samples from table</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_samples '$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 samples 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> + <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."/> + </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/> + <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. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>