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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 filter.
     arguments will    The optional `where` parameter may be used to filter
     be merged)        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).
  --citations          Show citations and exit.
  --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.