# Name of your program
package "RNALfoldz" # don't use package if you're using automake
purpose "calculate locally stable secondary structures of RNAs and there z-score"
#usage "RNALfoldz [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=RNALfoldz_cmdl --include-getopt --default-optional --func-name=RNALfoldz_cmdline_parser --arg-struct-name=RNALfoldz_args_info"


description "Computes 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"
int
default="150"
optional

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

option  "zscore"  z
"Set the minimal z-score threshold\nDue to parsing the commandline parameters a negative value should be given immediately after \"z\" without spaces\
 e.g. -z-4.9\n"
double
default="-2"
optional

section "Model Details"

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

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 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"
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 "See also:\n\nRNAplfold(1)\n\n"

text    "References:\n\nThe calculation of mfe structures is based on dynamic programming algorithm originally\
 developed by M. Zuker and P. Stiegler.\nThe partition function algorithm is based on work by J.S. McCaskill.\n\n
 The energy parameters are taken from:\n\nD.H. Mathews, J. Sabina, M. Zuker and H. Turner \"Expanded\
 Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure\",  JMB, 288, pp\
 911-940, 1999\n\nA. Walter, D Turner, J Kim, M Lyttle, P M\252ller, D Mathews, M Zuker \"Coaxial stacking of\
 helices enhances binding of oligoribonucleotides.\"\nPNAS, 91, pp 9218-9222, 1994\n\n\
 If 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\nM. Zuker, P. Stiegler (1981) \"Optimal computer folding of large RNA sequences using thermodynamic\
 and auxiliary information\", Nucl Acid Res 9: 133-148\n\nI.L. Hofacker, B. Priwitzer, and P.F. Stadler, \"Prediction of\
 Locally Stable RNA Secondary Structures for Genome-Wide Surveys\", Bioinformatics, 20, 186-190 (2004)\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"