qiime taxa filter-table (version 2019.4)

--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required]:

--p-include: TEXT One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]:

--p-exclude: TEXT One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]:

--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']:

--p-mode: :

Taxonomy-based feature table filter.

This method filters features from a table based on their taxonomic annotations. Features can be retained in the resulting table by specifying one or more include search terms, and can be filtered out of the resulting table by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided. Any samples that have a total frequency of zero after filtering will be removed from the resulting table.

Parameters

table : FeatureTable[Frequency]: Feature table to be filtered.
taxonomy : FeatureData[Taxonomy]: Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table will be ignored.
include : Str, optional: One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.
exclude : Str, optional: One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.
query_delimiter : Str, optional: The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.
mode : Str % Choices('exact', 'contains'), optional: Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term.

Returns

filtered_table : FeatureTable[Frequency]: The taxonomy-filtered feature table.