filter-features: Filter fragments in tree from table.¶

Docstring:

Usage: qiime fragment-insertion filter-features [OPTIONS]

  Filters fragments not inserted into a phylogenetic tree from a feature-
  table. Some fragments computed by e.g. Deblur or DADA2 are too remote to get
  inserted by SEPP into a reference phylogeny. To be able to use the feature-
  table for downstream analyses like computing Faith's PD or UniFrac, the
  feature-table must be cleared of fragments that are not part of the
  phylogenetic tree, because their path length can otherwise not be
  determined. Typically, the number of rejected fragments is low (<= 10), but
  it might be worth to inspect the ratio of reads assigned to those rejected
  fragments.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                         A feature-table which needs to filtered down to
                         those fragments that are contained in the tree, e.g.
                         result of a Deblur or DADA2 run.           [required]
  --i-tree ARTIFACT      The tree resulting from inserting fragments into a
    Phylogeny[Rooted]    reference phylogeny, i.e. the output of function
                         'sepp'                                     [required]
Outputs:
  --o-filtered-table ARTIFACT FeatureTable[Frequency]
                         The input table minus those fragments that were not
                         part of the tree. This feature-table can be used for
                         downstream analyses like phylogenetic alpha- or beta-
                         diversity computation.                     [required]
  --o-removed-table ARTIFACT FeatureTable[Frequency]
                         Those fragments that got removed from the input
                         table, because they were not part of the tree. This
                         table is mainly used for quality control, e.g. to
                         inspect the ratio of removed reads per sample from
                         the input table. You can ignore this table for
                         downstream analyses.                       [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.