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filter-samples: Filter samples out of demultiplexed data.

Docstring:

Usage: qiime demux filter-samples [OPTIONS]

  Filter samples indicated in given metadata out of demultiplexed data.
  Specific samples can be further selected with the WHERE clause, and the
  `exclude_ids` parameter allows for filtering of all samples not specified.

Inputs:
  --i-demux ARTIFACT SampleData[SequencesWithQuality¹ |
    PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
                         The demultiplexed data from which samples should be
                         filtered.                                  [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple            Sample metadata indicating which sample ids to
     arguments will be   filter. The optional `where` parameter may be used to
     merged)             filter ids based on specified conditions in the
                         metadata. The optional `exclude-ids` parameter may be
                         used to exclude the ids specified in the metadata
                         from the filter.                           [required]
  --p-where TEXT         Optional SQLite WHERE clause specifying sample
                         metadata criteria that must be met to be included in
                         the filtered data. If not provided, all samples in
                         `metadata` that are also in the demultiplexed data
                         will be retained.                          [optional]
  --p-exclude-ids / --p-no-exclude-ids
                         Defaults to False. If True, the samples selected by
                         the `metadata` and optional `where` parameter will be
                         excluded from the filtered data.     [default: False]
Outputs:
  --o-filtered-demux ARTIFACT SampleData[SequencesWithQuality¹ |
    PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
                         Filtered demultiplexed data.               [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.demux.methods import filter_samples

Docstring:

Filter samples out of demultiplexed data.

Filter samples indicated in given metadata out of demultiplexed data.
Specific samples can be further selected with the WHERE clause, and the
`exclude_ids` parameter allows for filtering of all samples not specified.

Parameters
----------
demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
    The demultiplexed data from which samples should be filtered.
metadata : Metadata
    Sample metadata indicating which sample ids to filter. The optional
    `where` parameter may be used to filter ids based on specified
    conditions in the metadata. The optional `exclude_ids` parameter may be
    used to exclude the ids specified in the metadata from the filter.
where : Str, optional
    Optional SQLite WHERE clause specifying sample metadata criteria that
    must be met to be included in the filtered data. If not provided, all
    samples in `metadata` that are also in the demultiplexed data will be
    retained.
exclude_ids : Bool, optional
    Defaults to False. If True, the samples selected by the `metadata` and
    optional `where` parameter will be excluded from the filtered data.

Returns
-------
filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
    Filtered demultiplexed data.