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filter-alpha-diversity: Filter samples from an alpha diversity metric.ΒΆ

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]