# Name of your program
package "RNApdist" # don't use package if you're using automake

purpose "Calculate distances between thermodynamic RNA secondary structures ensembles"

#usage "RNApdist [options]\n"
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNApdist_cmdl --include-getopt --default-optional --func-name=RNApdist_cmdline_parser --arg-struct-name=RNApdist_args_info"


description "This program reads RNA sequences from stdin and calculates structure\
 distances between the thermodynamic ensembles of their secondary structures.\n"

# Options
section "General Options"

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

section "Algorithms"

option    "compare"     X
"Specify the comparison directive.\n"
details="Possible arguments for this option are: -Xp compare the structures\
 pairwise (p), i.e. first with 2nd, third with 4th etc.\n-Xm calculate the\
 distance matrix between all structures. The output is formatted as a lower\
 triangle matrix.\n-Xf compare each structure to the first one.\n-Xc compare\
 continuously, that is i-th with (i+1)th structure.\n\n"
string
typestr="p|m|f|c"
default="p"
optional

option  "backtrack"     B
"Print an \"alignment\" with gaps of the profiles. The aligned structures\
 are written to <filename>, if specified.\n"
details="Within the profile output, the following symbols will be used:\n\n\
 ()  essentially upstream (downstream) paired bases\n\n\
 {}  weakly upstream (downstream) paired bases\n\n\
 |    strongly paired bases without preference\n\n\
 ,    weakly paired bases without preference\n\n\
 .    essentially unpaired bases.\n\n\
 If <filename> is not specified, the output is written to stdout,\
 unless the \"-Xm\" option is set in which case \"backtrack.file\" is used.\n\n"
string
typestr="<filename>"
argoptional
default="none"
optional

section "Model Details"

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

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
"set energy model for treatment of dangling bases\n\n"
int
default="2" 
values="0","2"

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

option  "noClosingGU" -
"Do not allow GU pairs at the end of helices\n\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\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\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\n"
int
optional
hidden




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