# Name of your program
package "RNAdistance" # don't use package if you're using automake

purpose "Calculate distances between RNA secondary structures"

#usage "RNAfold [options]\n"
#version "2.0"   # don't use version if you're using automake


# command line options passed to gengetopt
args "--file-name=RNAdistance_cmdl --include-getopt --default-optional --func-name=RNAdistance_cmdline_parser --arg-struct-name=RNAdistance_args_info"


description "This program reads RNA secondary structures from stdin and calculates one or more\
 measures for their dissimilarity, based on tree or string editing\
 (alignment). In addition it calculates a \"base pair distance\" given by the\
 number of base pairs present in one structure, but not the other. For\
 structures of different length base pair distance is not recommended.\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


option    "distance"    D
"Specify the distance representation to be used in calculations.\n"
details="Use the full, HIT, weighted coarse, or coarse representation to\
 calculate the distance. Capital letters indicate string alignment\
 otherwise tree editing is used.\nAny combination of distances can be\
specified.\n\n"
string
typestr="fhwcFHWCP"
default="f"
optional

option    "compare"     X
"Specify the comparison directive.\n"
details="Possible arguments for this option are: -Xp compare the structures\
 pairwise (p), i.e. first with 2nd, third with 4th etc.\n-Xm calculate the\
 distance matrix between all structures. The output is formatted as a lower\
 triangle matrix.\n-Xf compare each structure to the first one.\n-Xc compare\
 continuously, that is i-th with (i+1)th structure.\n\n"
string
typestr="p|m|f|c"
default="p"
optional

option  "shapiro"       S
"Use the Bruce Shapiro's cost matrix for comparing coarse structures.\n\n"
flag
off

option  "backtrack"     B
"Print an \"alignment\" with gaps of the structures, to show matching\
 substructures. The aligned structures are written to <filename>, if\
 specified.\n"
details="If <filename> is not specified, the output is written to stdout,\
 unless the -Xm option is set in which case \"backtrack.file\" is used.\n\n"
string
typestr="<filename>"
argoptional
default="none"
optional


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="RNAdist.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"
