decontam-identify: Identify contaminants¶

Docstring:

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

  This method 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]
Parameters:
  --m-metadata-file METADATA...
    (multiple            metadata file indicating which samples in the
     arguments will be   experiment are control samples, assumes sample names
     merged)             in file correspond to the `table` input parameter
                                                                    [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
                                                       [default: 'prevalence']
  --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]
Outputs:
  --o-decontam-scores ARTIFACT 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]
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.