# 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

option  "verbose" v
"Be verbose.\n"
details="Lower the log level setting such that even INFO messages are passed through.\n\n"
flag
off


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 internal 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 internal 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


option  "log-level" -
"Set log level threshold.\n"
details="By default, any log messages are filtered such that only warnings (level 2) or errors (level 3)\
 are printed. This setting allows for specifying the log level threshold, where higher values result in\
 fewer information. Log-level 5 turns off all messages, even errors and other critical information.\n\n"
int
typestr="level"
default="2"
hidden


option  "log-file" -
"Print log messages to a file instead of stderr.\n"
string
typestr="filename"
default="RNAparconv.log"
argoptional
hidden


option  "log-time" -
"Include time stamp in log messages.\n\n"
flag
off
hidden


option  "log-call" -
"Include file and line of log calling function.\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"
