# Name of your program
package "RNALfold" # don't use package if you're using automake
purpose "calculate locally stable secondary structures of RNAs"
#usage "RNALfold [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=RNALfold_cmdl --include-getopt --default-optional --func-name=RNALfold_cmdline_parser --arg-struct-name=RNALfold_args_info"


description "Compute locally stable RNA secondary structure with a maximal base pair\
 span. For a sequence of length n and a base pair span of L the algorithm uses only\
 O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to \"scan\" very large\
 genomes for short RNA structures.\nOutput consists of a list of secondary structure\
 components of size <= L, one entry per line. Each output line contains the predicted\
 local structure its energy in kcal/mol and the starting position of the local structure.\n"

# Options

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

option  "span"  L
"Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with\
 j-i>span will be allowed.\n\n"
int
default="150"
optional

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

section "Algorithms"
sectiondesc="Select additional algorithms which should be included in the calculations.\nThe Minimum free energy\
 (MFE) and a structure representative are calculated in any case.\n\n"

option  "zscore"  z
"Activate z-score computation. An optional argument may be supplied to set the threshold\nDue to parsing the\
 commandline parameters a negative value should be given immediately after \"z\" without spaces e.g. -z-4.9\n\n"
double
default="-2"
argoptional
optional

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


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
"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 the\
 default for mfe folding but 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\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\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"