# Name of your program
package "RNAheat" # don't use package if you're using automake
purpose "calculate specific heat of RNAs"
usage "RNAheat [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=RNAheat_cmdl --include-getopt --default-optional --func-name=RNAheat_cmdline_parser --arg-struct-name=RNAheat_args_info"


description "Reads RNA sequences from stdin and calculates their specific heat in the temperature range t1\
 to t2, from the partition function by numeric differentiation. The result is written to stdout as a list\
 of pairs of temperature in C and specific heat in Kcal/(Mol*K).\nThe program will continue to read new\
 sequences until a line consisting of the single character \"@\" or an end of file condition is encountered.\n"

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

option  "Tmin"  -
"Lowest temperature\n"
float
default = "0"
typestr="t1"

option  "Tmax"  -
"Highest temperature\n"
float
default = "100"
typestr="t2"

option "stepsize" -
"Calculate partition function every stepsize degrees C\n"
float
default="1."

option "ipoints" m
"The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter\
 produces a smoother curve\n"
int
typestr="ipoints"
default="2"

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

section "Model Details"

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 -d2 dangling energies will be added for the bases adjacent to a helix on both sides\
 in any case\n\n-d0 ignores dangling ends altogether (mostly for debugging).\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

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
hidden

text    "References:\n\nThe partition function algorithm is based on work by J.S. McCaskill.\n\n\
 J.S. McCaskill, (1990), \"The equilibrium partition function and base\
 pair binding probabilities for RNA secondary structures\", Biopolymers 29: 1105-1119\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\nD. Adams, (1979), \"The hitchhiker's guide\
 to the galaxy\", Pan Books, London\n\n"

text    "See also:\n\nRNAfold(1)\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"