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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
.TH CLONALORIGIN-GUI "1" "December 2017" "clonalorigin-gui 1.0" "User Commands"
.SH NAME
clonalorigin-gui \- GUI for clonalorigin
.SH Synopsis
.B clonalorigin-gui
[OPTIONS] <filename>
.SH DESCRIPTION
For graphical use, no options are necessary.
To pre\-run a limited set of functions, or use batch
mode, the following options can be used.
NOTE: They are processed IN ORDER, so be sure to open
the file before using it, and set output names before
producing the output!
.SH OPTIONS
.TP
\fB\-b\fR Batch mode. Perform operations then quit
.IP
without displaying the gui.
.TP
\fB\-o\fR <filename>
Open the specified input XML file.
.TP
\fB\-c\fR <filename><:num>
Write a csv file of the main features. If
:num is provided then it changes the variables
in the output (default 2):
.IP
:1 \- Parameters only
.IP
:2 \- Parameters + Number of recedges
.IP
:3 \- Parameters + Clonal Pairwise Distances
.IP
:4 \- All of the above.
.TP
\fB\-T\fR <filename>
Redirect the batch processed output
from stdout to the file specified.
Specify to display to the gui.
.TP
\fB\-t\fR <list>
Perform a convergence of trees test
between the open file and the set of
specified files (separated by commas).
.TP
\fB\-g\fR <list><:num> Perform a gelman\-rubin test
between the open file and the set of
specified files (separated by commas).
<num> takes the same meaning as for \fB\-c\fR.
.TP
\fB\-S\fR <filename>
Redirect the Score against true tree output
from stdout to the file specified.
Specify to display to the gui.
.TP
\fB\-s\fR <filename>
Perform a score against true tree test
against the newick\-format file specified.
.TP
\fB\-C\fR <i>
Performs a consensus\-of\-trees either with
the specified cutoff (integer i=0\-100) or
an extended consensus if i<0.
.TP
\fB\-H\fR 0/1/2/3
Extract the heatmap. Pass 0 for no prior correction,
1 for correction in number of std, 2 for correction
measured in proportion or 3 for prior only.
.TP
\fB\-d\fR 0/1/2/3
Extract the pairwise clonal tree heatmap. Pass 0 for
no prior correction,
1 for correction in number of std, 2 for correction
measured in proportion or 3 for prior only.
.TP
\fB\-e\fR <operation>:<value>:<filename>
Extract iterations and thin. <operation> is either
either "thin" with value "x" to thin every
x'th iteration, or "extract" with value "x\-y" to extract
iterations between x and y. The outputfile is after
the final colon.
.TP
\fB\-E\fR <filenames>:<filename>
Combines the list of output files specified NOT
including the current one, separated by commas, and
outputs to the file after the colon.
.TP
\fB\-n\fR
Start in the display mode without recombination (You must
specify the outputfile with \fB\-o\fR).
.TP
\fB\-h\fR
This help message.
.PP
.SH EXAMPLES
.HP
\fB\-o\fR test1.xml \fB\-t\fR test2.xml \fB\-b\fR:
.IP
Performs a convergence of tree test between files
test1.xml and test2.xml, printing the results to
stdout and exiting the program.
.HP
\fB\-o\fR test1.xml \fB\-t\fR test2.xml:
.IP
As above, but leave the gui window open.
.HP
\fB\-o\fR test1.xml \fB\-T\fR \fB\-t\fR test2.xml:
.IP
As above, but opens the results in the gui
and with the gui window open.
.HP
\fB\-o\fR test1.xml \fB\-t\fR test2.xml,test3.xml \fB\-b\fR:
.IP
Performs a convergence of tree test between files
test1.xml, test2.xml and test3.xml.
.HP
\fB\-t\fR test1.xml \fB\-o\fR test2.xml \fB\-b\fR:
.IP
Fails.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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