# Name of your program
package "RNAparconv" # don't use package if you're using automake
purpose "Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format"
usage "RNAparconv [options] [<input file>] [<output file>]\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=RNAparconv_cmdl --include-getopt --default-optional --unamed-opts --func-name=RNAparconv_cmdline_parser --arg-struct-name=RNAparconv_args_info"


description "Converts energy parameter files from \"old\" ViennaRNAPackage 1.8.4 format to\
 the new format used since ViennaRNAPackage 2.0.\nThe Program reads a valid energy parameter\
 file or valid energy parameters from stdin and prints the converted energy parameters to\
 stdout or a specified output file. Per default, the converted output file contains the whole\
 set of energy parameters used throughout ViennaRNAPackage 1.8.4. The user can specify sets of\
 energy parameters that should not be included in the output.\n"

# Options

section "I/O Options"
sectiondesc="Command line options for input and output (pre-)processing\n\n"

option  "input"  i
"Specify an input file name. If argument is missing the energy parameter input can be supplied via 'stdin'.\n\n"
string
typestr="filename"
optional

option  "output"  o
"Specify an output file name. If argument is missing the converted energy parameters are printed to 'stdout'.\n\n"
string
typestr="filename"
optional

option  "vanilla" -
"Print just as much as needed to represent the given energy parameters data set.\nThis option overrides all other output settings!\n\n"
flag
off

option  "dump" -
"Just dump Vienna 1.8.4 energy parameters in format used since 2.0.\nThis option skips any energy parameter input!\n\n"
flag
off

option  "silent" -
"Print just energy parameters and appropriate comment lines but suppress all other output\n\n"
flag
off

option  "without-HairpinE"  -
"Do not print converted hairpin energies and enthalpies\n\n"
flag
off
hidden

option  "without-StackE"  -
"Do not print converted stacking energies and enthalpies\n\n"
flag
off
hidden

option  "without-IntE"  -
"Do not print converted interior loop energies, enthalpies and asymetry factors\n\n"
flag
off
hidden

option  "without-BulgeE"  -
"Do not print converted bulge loop energies and enthalpies\n\n"
flag
off
hidden

option  "without-MultiE"  -
"Do not print converted multi loop energies and enthalpies\n\n"
flag
off
hidden

option  "without-MismatchE"  -
"Do not print converted exterior loop mismatch energies and enthalpies\n\n"
flag
off
hidden

option  "without-MismatchH"  -
"Do not print converted hairpin mismatch energies and enthalpies\n\n"
flag
off
hidden

option  "without-MismatchI"  -
"Do not print converted interior loop mismatch energies and enthalpies\n\n"
flag
off
hidden

option  "without-MismatchM"  -
"Do not print converted multi loop mismatch energies and enthalpies\n\n"
flag
off
hidden

option  "without-Dangle5"  -
"Do not print converted 5' dangle energies and enthalpies\n\n"
flag
off
hidden

option  "without-Dangle3"  -
"Do not print converted 3' dangle energies and enthalpies\n\n"
flag
off
hidden

option  "without-Misc"  -
"Do not print converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc)\n\n"
flag
off
hidden


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