# Name of your program
package "RNAduplex" # don't use package if you're using automake
purpose "Compute the structure upon hybridization of two RNA strands"
#usage "RNAduplex [options]\n"

# 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=RNAduplex_cmdl --include-getopt --default-optional --func-name=RNAduplex_cmdline_parser --arg-struct-name=RNAduplex_args_info"


description "reads two RNA sequences from stdin or <filename> and computes optimal\
 and suboptimal secondary structures for their hybridization. The calculation is simplified\
 by allowing only inter-molecular base pairs, for the general case use RNAcofold.\nThe computed\
 optimal and suboptimal structure 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"

# Options
section "General Options"
sectiondesc="Below are command line options which alter the general behavior of this program\n"

option  "sorted"  s
"print output sorted by free energy\n"
flag
off

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

section "Algorithms"
sectiondesc="Select additional algorithms which should be included in the calculations.\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"
float
typestr="range"
optional

section "Model Details"

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

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

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, this is unsupported\
 for the partition function folding.\n\nWith -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 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 interior pairs in a loop of degree 3\
 and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
 treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
 energy model.\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"
flag
off

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

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

option  "paramFile" P
"Read energy parameters from paramfile, instead of using the default parameter set.\n"
details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
 documentation for details on the file format.\n"
string
typestr="paramfile"
optional

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.\ne.g.\
 RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
 energy.\n"
string
optional
hidden

text    "See also:\n\nRNAcofold(l) RNAfold(l)\n\n"
text    "Written by:\n\nIvo L Hofacker\n\n"
text    "Report bugs:\n\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
 rna@tbi.univie.ac.at.\n"