NAME

       ktImportPhymmBL - explore hierarchical metagenomic data with zoomable pie charts

DESCRIPTION

       Creates  a  Krona  chart  of  Phymm  or  PhymmBL results. Note: Since confidence scores are not given for
       species/subspecies classifications, they inheret confidence scores from genus classifications.

       ktImportPhymmBL \

              [options]               \               phymmbl_results_1[:magnitudes_1][,name_1]                \
              [phymmbl_results_2[:magnitudes_2][,name_2]] \ ...

       phymmbl_results
              PhymmBL  results  files  (results.03.*).  Results can also be from Phymm alone (results.01.*), but
              [-p] must be specified. 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: 'phymm(bl).krona.html']

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

       [-m <number>]
              Minimum confidence. Each query sequence will only be added to taxa  that  were  predicted  with  a
              confidence score of at least this value.

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

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

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

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

       [-p]   Input is phymm only (no confidence scores).

       [-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.