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filter-alpha-diversity: Filter samples from an alpha diversity metric.¶
Docstring:
Usage: qiime diversity filter-alpha-diversity [OPTIONS]
Filter samples from an alpha diversity metric, retaining samples with
corresponding `metadata` (or retaining samples without metadata, if
`exclude_ids` is True). See the filtering tutorial on
https://docs.qiime2.org for additional details.
Inputs:
--i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
Alpha diversity sample data to filter by sample.
[required]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata used to select samples to retain
arguments will be from the sample data (default) or select samples to
merged) exclude using the `exclude-ids` parameter. [required]
--p-where TEXT SQLite WHERE clause specifying sample metadata
criteria that must be met to be included in the
filtered alpha diversity artifact. If not provided,
all samples in `metadata` that are also in the input
alpha diversity artifact will be retained. [optional]
--p-exclude-ids / --p-no-exclude-ids
If `True`, the samples selected by `metadata` or the
`where` parameters will be excluded from the filtered
alpha diversity artifact instead of being retained.
[default: False]
Outputs:
--o-filtered-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.diversity.methods import filter_alpha_diversity
Docstring:
Filter samples from an alpha diversity metric.
Filter samples from an alpha diversity metric, retaining samples with
corresponding `metadata` (or retaining samples without metadata, if
`exclude_ids` is True). See the filtering tutorial on
https://docs.qiime2.org for additional details.
Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
Alpha diversity sample data to filter by sample.
metadata : Metadata
Sample metadata used to select samples to retain from the sample data
(default) or select samples to exclude using the `exclude_ids`
parameter.
where : Str, optional
SQLite WHERE clause specifying sample metadata criteria that must be
met to be included in the filtered alpha diversity artifact. If not
provided, all samples in `metadata` that are also in the input alpha
diversity artifact will be retained.
exclude_ids : Bool, optional
If `True`, the samples selected by `metadata` or the `where` parameters
will be excluded from the filtered alpha diversity artifact instead of
being retained.
Returns
-------
filtered_alpha_diversity : SampleData[AlphaDiversity]