NAME

       ktImportTaxonomy - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION

              Creates a Krona chart based on taxonomy IDs and, optionally, magnitudes and scores.
              Taxonomy IDs corresponding to a rank of "no rank" in the database will be  assigned
              to  their  parents  to make the hierarchy less cluttered (e.g. "Cellular organisms"
              will be assigned to "root").

              ktImportTaxonomy \

              [options]            \             taxonomy_1[:magnitudes_1][,name_1]             \
              [taxonomy_2[:magnitudes_2][,name_2]] \ ...

       taxonomy
              Tab-delimited  file  with  taxonomy  IDs and (optionally) query IDs, magnitudes and
              scores. By default, query IDs, taxonomy IDs and scores will be taken  from  columns
              1, 2 and 3, respectively (see -q, -t, -s, and -m). Lines beginning with "#" will be
              ignored. By default, separate datasets will be created for each input (see [-c]).

       magnitudes
              Optional file listing query IDs with magnitudes, separated by  tabs.  This  can  be
              used  to  account  for  read  length  or  contig  depth  to  obtain a more accurate
              representation  of  abundance.  By  default,  query  sequences  without   specified
              magnitudes will be assigned a magnitude of 1. Magnitude files for assemblies in ACE
              format can be created with ktGetContigMagnitudes.

       name   A name to show in the list of datasets in the Krona chart (if multiple input  files
              are  present  and [-c] is not specified). By default, the basename of the file will
              be used.

       [-o <string>]
              Output file name. [Default: 'taxonomy.krona.html']

       [-n <string>]
              Name of the highest level. [Default: 'Root']

       [-i]   Include a wedge for queries with no hits.

       [-c]   Combine data from each file, rather than  creating  separate  datasets  within  the
              chart.

       [-q <integer>]
              Column  of  input  files  to  use  as  query  ID.  Required  if magnitude files are
              specified. [Default: '1']

       [-t <integer>]
              Column of input files to use as taxonomy ID. [Default: '2']

       [-s <integer>]
              Column of input files to use as score. [Default: '3']

       [-m <integer>]
              Column of input files to use as magnitude. If magnitude files are specified,  their
              magnitudes will override those in this column.

       [-d <integer>]
              Maximum depth of wedges to include in the chart.

       [-k]   Show the "cellular organisms" taxon (collapsed by default).

       [-K]   Collapse assignments to taxa with ranks labeled "no rank" by moving up to parent.

       [-x <integer>]
              Hue (0-360) for "bad" scores. [Default: '0']

       [-y <integer>]
              Hue (0-360) for "good" scores. [Default: '120']

       [-u <string>]
              URL  of  Krona  resources  to  use  instead  of  bundling them with the chart (e.g.
              "http://krona.sourceforge.net"). Reduces size of charts and allows updates,  though
              charts will not work without access to this URL.

       [-qp <string>]
              Url  to  send  query IDs to (instead of listing them) for each wedge. The query IDs
              will be sent as a comma separated list in the POST  variable  "queries",  with  the
              current  dataset index (from 0) in the POST variable "dataset". The url can include
              additional variables encoded via GET.

       [-tax <string>]
              Path  to   directory   containing   a   taxonomy   database   to   use.   [Default:
              '/usr/share/perl5/KronaTools/taxonomy']