# Name of your program
package "RNA2Dfold" # don't use package if you're using automake
purpose "Compute MFE structure, partition function and representative sample structures of k,l neighborhoods"

# Version of your program
#version "0.9"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNA2Dfold_cmdl --include-getopt --default-optional --func-name=RNA2Dfold_cmdline_parser --arg-struct-name=RNA2Dfold_args_info"

description "The program partitions the secondary structure space into (basepair)distance classes according to\
 two fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as\
 its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is\
 computed. Additionally, a stochastic backtracking routine allows one to produce samples of representative suboptimal\
 secondary structures from each partition\n\n"


# Options

option  "verbose" v
"Be verbose.\n"
details="Lower the log level setting such that even INFO messages are passed through.\n\n"
flag
off


section "I/O Options"
sectiondesc="Command line options for input and output (pre-)processing\n\n"

option  "numThreads"  j
"Set the number of threads used for calculations (only available when compiled with OpenMP support)\n\n"
int
optional

option  "noconv"  -
"Do not automatically substitute nucleotide \"T\" with \"U\".\n\n"
flag
off


option  "log-level" -
"Set log level threshold.\n"
details="By default, any log messages are filtered such that only warnings (level 2) or errors (level 3)\
 are printed. This setting allows for specifying the log level threshold, where higher values result in\
 fewer information. Log-level 5 turns off all messages, even errors and other critical information.\n\n"
int
typestr="level"
default="2"
hidden


option  "log-file" -
"Print log messages to a file instead of stderr.\n"
string
typestr="filename"
default="RNA2Dfold.log"
argoptional
hidden


option  "log-time" -
"Include time stamp in log messages.\n\n"
flag
off
hidden


option  "log-call" -
"Include file and line of log calling function.\n\n"
flag
off
hidden


section "Algorithms"
sectiondesc="Select additional algorithms which should be included in the calculations.\nThe Minimum free energy\
 (MFE) and a structure representative are calculated in any case.\n\n"

option  "partfunc"  p
"calculate partition function and thus, Boltzmann probabilities and Gibbs free energy\n\n"
flag
off

option  "stochBT" -
"backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s)\n\n"
int
optional

option  "neighborhood"  -
"backtrack structures from certain k,l-neighborhood only, can be specified multiple times (<k>:<l>,<m>:<n>,...)\n\n"
string
typestr="<k>:<l>"
multiple
dependon="stochBT"

option  "maxDist1"  K
"maximum distance to first reference structure"
details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
 be thrown into a distance class denoted by K=L=-1\n\n"
int
optional

option  "maxDist2"  L
"maximum distance to second reference structure"
details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
 be thrown into a distance class denoted by K=L=-1\n\n"
int 

option  "pfScale" S
"In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid\
 overflows).\n"
details="The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences.\n\n"
double
default="1.07"
optional
hidden

option  "noBT"  -
"do not backtrack structures, calculate energy contributions only\n\n"
flag
off

option  "circ"    c
"Assume a circular (instead of linear) RNA molecule.\n\n"
flag
off



section "Energy Parameters"
sectiondesc="Energy parameter sets can be adapted or loaded from user-provided input files\n\n"

option  "temp"  T
"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
double
default="37.0"
optional

option  "paramFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="Different sets of energy parameters for RNA and DNA should accompany your distribution.\nSee the\
 RNAlib documentation for details on the file format. The placeholder file name 'DNA' can be used\
 to load DNA parameters without the need to actually specify any input file.\n\n"
string
typestr="paramfile"
optional

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins.\n"
details="Mostly for testing.\n\n"
flag
off
hidden

option  "salt" -
"Set salt concentration in molar (M). Default is 1.021M.\n\n"
double
optional


section "Model Details"
sectiondesc="Tweak the energy model and pairing rules additionally using the following parameters\n\n"

option  "dangles" d
"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
details="\nWith -d2 dangling energies will be added for the bases adjacent to a helix on both sides\
 in any case. The option -d0 ignores dangling ends altogether (mostly for debugging).\n\n"
int
default="2"
values="0","2"
optional

option  "noGU"  -
"Do not allow GU pairs.\n\n"
flag
off
hidden

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices.\n\n"
flag
off
hidden

option  "helical-rise"  -
"Set the helical rise of the helix in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 3.4 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="2.8"
hidden

option  "backbone-length"  -
"Set the average backbone length for looped regions in units of Angstrom.\n"
details="Use with caution! This value will be re-set automatically to 6.76 in case DNA\
 parameters are loaded via -P DNA and no further value is provided.\n\n"
float
optional
default="6.0"
hidden


text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at.\n\n"
