# Name of your program
package "RNAeval" # don't use package if you're using automake
purpose "calculate energy of RNA sequences with given secondary structure"
#usage "RNAeval [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=RNAeval_cmdl --include-getopt --default-optional --func-name=RNAeval_cmdline_parser --arg-struct-name=RNAeval_args_info"


description "Evaluates the free energy of an RNA molecule in fixed secondary structure.\
 Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written\
 to stdout.\nThe program will continue to read new sequences and structures until a line\
 consisting of the single character \"@\" or an end of file condition is encountered.\nIf\
 the input sequence or structure contains the separator character \"&\" the program calculates\
 the energy of the co-folding of two RNA strands, where the \"&\" marks the boundary between\
 the two strands.\n"

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

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

option "verbose" v
"Print out energy contribution of each loop in the structure.\n\n"
flag
off

section "Model Details"

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

option  "noTetra" 4
"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\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 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.\n"
int
default="2"
optional

option  "energyModel" e
"Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
 A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
int
optional

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\n"
string
typestr="paramfile"
optional

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

option  "gquad" g
"Incoorporate G-Quadruplex formation into the structure prediction algorithm\n"
flag
off

option  "logML" -
"Recalculate energies of structures using a logarithmic energy function for multi-loops before output.\n"
details="This option does not effect structure generation, only the energies that are printed out.\
 Since logML lowers energies somewhat, some structures may be missing.\n\n"
flag
off

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