# The Global section of the configuration file contains all
# directives which affect all modules or set global paths

[global]

# The workdir is where Ortholuge will maintain all working
# files for the process and is the default directory for
# output to be placed.  If you are running multiple instances
# of Ortholuge, you should have one workdir for each
# analysis, to avoid instances overwriting each other.

workdir=/tmp/ortholuge

# Set the bindir if the Ortholuge scripts aren't in your
# path or you're not running Ortholuge from the install
# directory.

#bindir=./

# infile1, infile2, and outfile are the three input FASTA
# files needed for Ortholuge

infile1=ingroup1.fasta
infile2=ingroup2.fasta
outfile=outgroup.fasta

# ingroup1, ingroup1, and outgroup are the three labels for
# the input files on the graphs Ortholuge produces, these
# labels are optional

ingroup1=ingroup1
ingroup2=ingroup2
outgroup=ingroup3

# seqtype is the type of input file being given, this may
# be either protein or dna

seqtype=protein
#seqtype=dna

# Ortholuge has three levels of verbosity which may be set

verbose=0
#verbose=1
#verbose=2

# By default Ortholuge won't overwrite existing working
# directories and files, unless overwrite is set to 1.

overwrite=0

# The rbb section deals with options dealing with finding
# the reciprical best blast of the input files.

[rbb]

# skipblast allows you to run Ortholuge without performing
# the BLASTs, setting this to yes assumes you have the needed
# BLAST output files with the correct file names.  It's
# usually best to leave this option alone

skipblast=0

# By default the interm RBB output file is rbb.out in the
# workdir, this can be overridden with the outfile option

outfile=rbb.out

# The alignment section deals with options dealing with
# the multiple sequence alignment of the triplets

[alignment]

# By default, the interm output of the multiple sequence
# alignment is triplet.out in the workdir, this can be
# overridden with the outfile option

outfile=triplet.out

# If Muscle isn't in your default path, the muscle option
# can be used to point to the exact path AND filename of
# you Muscle executable

# muscle=muscle

# If eprotdist or ednadist isn't in you default path, the
# phylip option can be used to point to the exact path
# AND filename of the executable

#phylip=(eprotdist|ednadist)

# The histogram section deals with options surrounding
# the histogram output from Ortholuge

[histogram]

# By default, the output file for the histogram is
# ratios.svg or ratios.png in the workdir, this can
# be overridden with the outfile option

outfile=ratios.svg

# If grey is set to 1, the graph will be output in
# greyscale only

grey=0

# format sets the format of the output graph, the
# options are svg and png.  Note, the format MUST
# match the file extension of the outfile if it
# is set

format=svg
#format=png

# scale sets the maximum x-axis scale for the graph,
# if this is 0, the graph automatically scales to
# encompus all data points

scale=2.0

# The scatter section deals with options surrounding
# the scatter plot output from Ortholuge

[scatter]

# By default, the output file for the scatter plot is
# scatter.svg or scatter.png in the workdir, this can
# be overridden with the outfile option

outfile=scatter.svg

# format sets the format of the output graph, the
# options are svg and png.  Note, the format MUST
# match the file extension of the outfile if it
# is set

format=svg
#format=png

# scale sets the maximum x and y-axis scale for the graph,
# if this is 0, the graph automatically scales to
# encompus all data points

scale=2.0

# r1a and r2a set the x and y-axis values where the
# inner box (putative ortholuges) should be placed 
# on the scatter plot

#r1a=
#r2a=

# r1b and r2b set the x and y-axis values where the
# outter box (possible ortholuges) should be placed 
# on the scatter plot

#r1b=
#r2b=

# shade sets if the two ratio boxes on the graph 
# should be shaded or not

shade=0

# text sets if three files should be made for the
# listing the triplets in each of the three classes
# as layed out by r1a, r2a, r1b, and r2b.
# This is not yet implemented

text=0