.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH CGVIEW_COMPARISON_TOOL "1" "August 2018" "cgview_comparison_tool 20170919" "User Commands"
.SH NAME
cgview_comparison_tool \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
.SH DESCRIPTION
.SS "USAGE:"
.IP
cgview_comparison_tool \fB\-p\fR DIR [options]
.SS "DESCRIPTION:"
.IP
Run this command once to generate a project directory. After the project is
created place a reference genome in the reference_genome directory and any
genomes to compare with the reference in the comparison_genomes directory.
.IP
[Optional] Make changes to the project_settings.conf file to configure how
the maps will be drawn. Add additional GFF files to the features and
analyis directories.
.IP
Draw maps by running this command again with the '\-p' option pointing to
the project directory.
.SS "REQUIRED ARGUMENTS:"
.HP
\fB\-p\fR, \fB\-\-project\fR DIR
.IP
If no project exists yet, a blank project directory will be created.
If the project exists, maps will be created.
.PP
OPTIONAL ARGUMENTS:
.HP
\fB\-s\fR, \fB\-\-settings\fR FILE
.IP
The settings file. If none is provided, the default settings file will be
copied from \fI\,$CCT_HOME/conf/project_settings.conf\/\fP to the project
directory.
.HP
\fB\-g\fR, \fB\-\-config\fR FILE
.IP
The configuration file. The default is to use the
\fI\,$CCT_HOME/conf/global_settings.conf\/\fP file.
.HP
\fB\-z\fR, \fB\-\-map_size\fR STRING
.IP
Size of custom maps to create. For quickly generating new map sizes, use
this option with the \fB\-\-start_at_xml\fR option. Possible sizes include
small/medium/large/x\-large or a combination separated by commas (e.g.
small,large). The size(s) provided will override the size(s) in the
configuration files.
.HP
\fB\-x\fR, \fB\-\-start_at_xml\fR
.IP
Jump to XML generation. Skips performing blast, which can
speed map generation if blast has already been done. This option is for
creating new maps after making changes to the .conf files. Note that
any changes in the .conf files related to blast will be ignored.
.HP
\fB\-r\fR, \fB\-\-start_at_map\fR
.IP
Start at map generation. Skips performing blast and
generating XML. Useful if manual changes to the XML files have
been made or if creating new map sizes (see \fB\-\-map_size\fR).
.HP
\fB\-f\fR, \fB\-\-map_prefix\fR STRING
.IP
Prefix to be appended to map names (Default is to add no additional
prefix).
.HP
\fB\-b\fR, \fB\-\-max_blast_comparisons\fR INTEGER
.IP
The maximum number of BLAST results sets to be passed to the XML
creation phase (Default is 100).
.HP
\fB\-t\fR, \fB\-\-sort_blast_tracks\fR
.IP
Sort BLAST results such that genomes with highest similarity are plotted
first.
.HP
\fB\-\-cct\fR
.IP
Colour BLAST results based on percent identity of hit instead of by
source genome, and ignore 'use_opacity' setting in configuration file.
.HP
\fB\-m\fR, \fB\-\-memory\fR STRING
.IP
Memory string to pass to Java's '\-Xmx' option (Default is 1500m).
.HP
\fB\-c\fR, \fB\-\-custom\fR STRINGS
.IP
Settings used to customize the appearance of the map.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Show this message.
.SS "EXAMPLE:"
.IP
cgview_comparison_tool \fB\-p\fR my_project \fB\-b\fR 50 \fB\-t\fR \e
.HP
\fB\-\-custom\fR tickLength=20 labelFontSize=15 \fB\-\-map_size\fR medium,x\-large
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.