.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH KTIMPORTPHYMMBL "1" "June 2021" "ktImportPhymmBL 2.8" "User Commands"
.SH NAME
ktImportPhymmBL \- explore hierarchical metagenomic data with zoomable pie charts
.SH DESCRIPTION
.IP
.PP
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.
.IP
.PP
ktImportPhymmBL \e
.IP
[options] \e
phymmbl_results_1[:magnitudes_1][,name_1] \e
[phymmbl_results_2[:magnitudes_2][,name_2]] \e
\&...
.TP
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]).
.TP
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.
.TP
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.
.IP
.TP
[\-o <string>]
Output file name. [Default: 'phymm(bl).krona.html']
.TP
[\-n <string>]
Name of the highest level. [Default: 'all']
.TP
[\-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.
.TP
[\-c]
Combine data from each file, rather than creating separate datasets within the chart.
.TP
[\-d <integer>]
Maximum depth of wedges to include in the chart.
.TP
[\-x <integer>]
Hue (0\-360) for "bad" scores. [Default: '0']
.TP
[\-y <integer>]
Hue (0\-360) for "good" scores. [Default: '120']
.TP
[\-p]
Input is phymm only (no confidence scores).
.TP
[\-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.
.TP
[\-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.