decontam-score-viz: Generate a histogram representation of the scores¶

Docstring:

Usage: qiime quality-control decontam-score-viz [OPTIONS]

  Creates histogram based on the output of decontam identify

Inputs:
  --i-decontam-scores ARTIFACTS... Collection[FeatureData[DecontamScore]]
                          Output from decontam identify to be visualized
                                                                    [required]
  --i-table ARTIFACTS... Collection[FeatureTable[Frequency]]
                          Raw OTU/ASV table that was used as input to
                          decontam-identify                         [required]
  --i-rep-seqs ARTIFACT FeatureData[Sequence]
                          Representative Sequences table which contaminate
                          sequences will be removed from            [optional]
Parameters:
  --p-threshold PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          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 PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Select bin size for the histogram    [default: 0.02]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [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.