# Name of your program
package "RNAup" # don't use package if you're using automake
purpose "Calculate the thermodynamics of RNA-RNA interactions"
#usage "RNAup" [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=RNAup_cmdl --include-getopt --default-optional --func-name=RNAup_cmdline_parser --arg-struct-name=RNAup_args_info"


description "RNAup calculates the thermodynamics of RNA-RNA interactions, by decomposing the\
 binding into two stages. (1) First the probability that a potential binding sites remains\
 unpaired (equivalent to the free energy needed to open the site) is computed. (2) Then this\
 accessibility is combined with the interaction energy to obtain the total binding energy.\
 All calculations are done by computing partition functions over all possible conformations.\n"

# Options

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

option  "constraint"  C
"Calculate structures subject to constraints.\n"
details="The program reads first the\
 sequence(s), then a string containing constraints on the structure encoded with the symbols:\n\
 . (no constraint for this base)\n
 x (the base is unpaired)\n\
 < (base i is paired with a base j>i) (solely used for calculation of unpaired regions)\n\
 > (base i is paired with a base j<i) (solely used for calculation of unpaired regions)\n\
 ( ) (base i pairs base j)\n\
 | (the corresponding base has to be paired intermolecularily (works only in interaction mode)\n\n"
flag
off

option  "no_output_file" o
"Do not produce an output file\n\n"
flag
off

option  "no_header" -
"Do not produce a header with the command line parameters used in the outputfile\n\n"
flag
off

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

section "Calculations of opening energies"

option  "ulength"   u
"specifies the length of the unstructured region in the output.\n"
details="The probability of being unpaired is plotted on the right border\
 of the unpaired region. You can specify up to 20 different length values:\
 use \"-\" to specify a range of continuous values (e.g. -u 4-8) or specify\
 a list of comma separated values (e.g. -u 4,8,15).\n\n"
string
multiple
typestr="length"
default="4"
optional

option "contributions"  c
"Specify the contributions listed in the output\n"
details="By default only the full probability of being unpaired is plotted.\
 The -c option allows to get the different contributions (c) to the probability\
 of being unpaired: The full probability of being unpaired (\"S\" is the sum of\
 the probability of being unpaired in the exterior loop (\"E\"), within a\
 hairpin loop (\"H\"), within an interior loop (\"I\") and within a multiloop\
 (\"M\"). Any combination of these letters may be given.\n\n"
string
typestr="SHIME"
default="S"
optional

section "Calculations of RNA-RNA interactions"
option  "window"  w
"Determine the maximal length of the region of interaction\n\n"
int
default="25"
optional

option  "include_both"  b
"Include the probability of unpaired regions in both (b) RNAs. By default
only the probability of being unpaired in the longer RNA (target) is used.\n\n"
flag
off

option  "extend5" 5
"Extend the region of interaction in the target to some residues on the 5' side\n"
details="The underlying assumption is that it is favorable for an interaction if\
 not only the direct region of contact is unpaired but also a few residues 5'\n\n"
int
optional

option  "extend3" 3
"Extend the region of interaction in the target to some residues on the 3' side\n"
details="The underlying assumption is that it is favorable for an interaction if\
 not only the direct region of contact is unpaired but also a few residues 3'\n\n"
int
optional

option  "interaction_pairwise"  -
"Activate pairwise interaction mode\n"
details="The first sequence interacts with the 2nd, the third with the 4th etc.\
 If activated, two interacting sequences may be given in a single line separated\
 by \"&\" or each sequence may be given on an extra line.\n\n"
flag
off

option  "interaction_first" -
"Activate interaction mode using first sequence only\n"
details="The interaction of each sequence with the first one is calculated\
 (e.g. interaction of one mRNA with many small RNAs). Each sequence has to be\
 given on an extra line\n\n"
flag
off

section "Model Details"

option  "pfScale" S
"In the calculation of the pf use scale*mfe as an estimate for the ensemble\
 free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed\
 for long sequences.\nYou can also recompile the program to use double precision (see the README file).\n\n"
double
optional
hidden

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