decontam-identify-batches: Identify contaminants in Batch Mode¶

Docstring:

Usage: qiime quality-control decontam-identify-batches [OPTIONS]

  This method breaks an ASV table into batches based on the given metadata and
  identifies contaminant sequences from an OTU or ASV table and reports them
  to the user

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          Feature table which contaminate sequences will be
                          identified from                           [required]
  --i-rep-seqs ARTIFACT FeatureData[Sequence]
                          Representative Sequences table which contaminate
                          seqeunces will be removed from            [optional]
Parameters:
  --m-metadata-file METADATA...
    (multiple arguments   metadata file indicating which samples in the
     will be merged)      experiment are control samples, assumes sample names
                          in file correspond to the `table` input parameter
                                                                    [required]
  --p-split-column TEXT   input metadata columns that you wish to subset the
                          ASV table byNote: Column names must be in quotes and
                          delimited by a space                      [required]
  --p-method TEXT Choices('combined', 'frequency', 'prevalence')
                          Select how to which method to id contaminants with;
                          Prevalence: Utilizes control ASVs/OTUs to identify
                          contaminants, Frequency: Utilizes sample
                          concentration information to identify contaminants,
                          Combined: Utilizes both Prevalence and Frequency
                          methods when identifying contaminants     [required]
  --p-filter-empty-features / --p-no-filter-empty-features
                          If true, features which are not present in a split
                          feature table are dropped.                [optional]
  --p-freq-concentration-column TEXT
                          Input column name that has concentration
                          information for the samples               [optional]
  --p-prev-control-column TEXT
                          Input column name containing experimental or
                          control sample metadata                   [optional]
  --p-prev-control-indicator TEXT
                          indicate the control sample identifier (e.g.
                          "control" or "blank")                     [optional]
  --p-threshold NUMBER    Select threshold cutoff for decontam algorithm
                          scores                                [default: 0.1]
  --p-weighted / --p-no-weighted
                          weight the decontam scores by their associated read
                          number                               [default: True]
  --p-bin-size NUMBER     Select bin size for the histogram    [default: 0.02]
Outputs:
  --o-batch-subset-tables ARTIFACTS... Collection[FeatureTable[Frequency]]
                          Directory where feature tables split based on
                          metadata and parameter split-column values should be
                          written.                                  [required]
  --o-decontam-scores ARTIFACTS... Collection[FeatureData[DecontamScore]]
                          The resulting table of scores from the decontam
                          algorithm which scores each feature on how likely
                          they are to be a contaminant sequence     [required]
  --o-score-histograms VISUALIZATION
                          The vizulaizer histograms for all decontam score
                          objects generated from the pipeline       [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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --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.