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.