weighted-unifrac: Weighted Unifrac¶

Docstring:

Usage: qiime diversity-lib weighted-unifrac [OPTIONS]

  Compute Weighted Unifrac for each sample in a feature table

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency]
                          The feature table containing the samples for which
                          Weighted Unifrac should be computed.      [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-threads NTHREADS    The number of CPU threads to use in performing this
                          calculation. May not exceed the number of available
                          physical cores. If threads = 'auto', one thread will
                          be created for each identified CPU core on the host.
                                                                  [default: 1]
  --p-bypass-tips / --p-no-bypass-tips
                          In a bifurcating tree, the tips make up about 50%
                          of the nodes in a tree. By ignoring them,
                          specificity can be traded for reduced compute time.
                          This has the effect of collapsing the phylogeny, and
                          is analogous (in concept) to moving from 99% to 97%
                          OTUs                                [default: False]
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix        Distance matrix for Unweighted Unifrac.   [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.

Examples:
  # ### example: run on one core (by default)
  qiime diversity-lib weighted-unifrac \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --o-distance-matrix weighted-unifrac-dm.qza

  # ### example: to run on n cores, replace 1 here with your preferred integer
  qiime diversity-lib weighted-unifrac \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-threads 1 \
    --o-distance-matrix weighted-unifrac-dm.qza

  # ### example: use 'auto' to run on all of host system's available CPU cores
  qiime diversity-lib weighted-unifrac \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-threads auto \
    --o-distance-matrix weighted-unifrac-dm.qza

  # ### example: use bypass tips to trade specificity for reduced compute time
  # bypass_tips can be used with any threads setting, but auto may be a good
  # choice if you're trimming run time.
  qiime diversity-lib weighted-unifrac \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --p-threads auto \
    --p-bypass-tips \
    --o-distance-matrix weighted-unifrac-dm.qza