# 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"
flag
off

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

section "Model Details"

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

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 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"
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"
string
typestr="paramfile"
optional

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

text    "References:\n\nIf you use this program in your work you might want to cite:\n\nI.L. Hofacker,\
 W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) \"Fast Folding and Comparison\
 of RNA Secondary Structures\", Monatshefte f. Chemie 125: 167-188\n\n"

text    "Written by\n\nIvo L Hofacker, Peter F Stadler.\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"