# Name of your program
package "RNAaliduplex" # don't use package if you're using automake
purpose "Predict conserved RNA-RNA interactions between two alignments"
usage "RNAaliduplex [options] <file1.aln> <file2.aln>"

# Version of your program
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNAaliduplex_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNAaliduplex_cmdline_parser --arg-struct-name=RNAaliduplex_args_info"


description "The program reads two alignments of RNA sequences in CLUSTAL format and predicts optimal and\
 suboptimal binding sites, hybridization energies and the corresponding structures. The calculation\
 takes only inter-molecular base pairs into account, for the general case use RNAcofold. The use of\
 alignments allows one to focus on binding sites that are evolutionary conserved. Note, that the two\
 input alignments need to have equal number of sequences and the same order, i.e. the 1st sequence\
 in file1 will be hybridized to the 1st in file2 etc.\n\nThe computed binding sites, energies, and\
 structures are written to stdout, one structure per line. Each line consist of: The structure in\
 dot bracket format with a \"&\" separating the two strands. The range of the structure in the two\
 sequences in the format  \"from,to : from,to\"; the energy of duplex structure in kcal/mol.\nThe\
 format is especially useful for computing the hybrid structure between a small probe sequence and\
 a long target sequence.\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 "Algorithms"
sectiondesc="Select additional algorithms which should be included in the calculations.\n\n"

option  "deltaEnergy" e
"Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\
 Default is calculation of mfe structure only.\n\n"
float
typestr="range"
optional

option  "sorted"  s
"Sort output by free energy.\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

option  "saltInit" -
"Provide salt correction for duplex initialization (in kcal/mol).\n\n"
double
optional
hidden


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 -d1 only unpaired bases can participate in at most one dangling end. With -d2 this\
 check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in\
 any case; this is the default for mfe and partition function folding (-p).\nThe option -d0 ignores\
 dangling ends altogether (mostly for debugging).\nWith -d3 mfe folding will allow coaxial stacking\
 of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking\
 of the two enclosed pairs in a loop of degree 3 and works only for mfe folding.\n\nNote that with\
 -d1 and -d3 only the MFE computations will be using this setting while partition function uses\
 -d2 setting, i.e. dangling ends will be treated differently.\n\n"
int
default="2"
optional

option  "noLP"  -
"Produce structures without lonely pairs (helices of length 1).\n"
details="For partition function folding this only disallows pairs that can only occur isolated. Other\
 pairs may still occasionally occur as helices of length 1.\n\n"
flag
off

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  "nsp" -
"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
details="Its argument is a comma separated list of additionally allowed pairs. If the\
 first character is a \"-\" then AB will imply that AB and BA are allowed pairs, e.g.\
 --nsp=\"-GA\"  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
 energy.\n\n"
string
optional
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


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="RNAaliduplex.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


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