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

purpose "Draw RNA Secondary Structures"

#usage "RNAplot [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=RNAplot_cmdl --include-getopt --default-optional --func-name=RNAplot_cmdline_parser --arg-struct-name=RNAplot_args_info"


description "The program reads RNA sequences and structures from stdin in the format as produced by\
 RNAfold and produces drawings of the secondary structure graph.\nThe coordinates are produced using\
 either E. Bruccoleri's naview routines, or a simple radial layout method.\n\nIf the sequence was\
 preceded by a line of the form\n\n>name\n\nthe output file will be named \"name_ss.ps\" otherwise\
 \"rna.ps\" is used.\nExisting files of the same name will be overwritten.\n"

# Options
option  "layout-type"  t
"Choose the layout algorithm. Simple radial layout if 0, or naview if 1\n\n"
int
default="1"
optional

option  "output-format"   o
"Specify output format. Available formats are: PostScript (ps), Graph Meta Language (gml),\
 Scalable Vector Graphics (svg), and XRNA save file (xrna). Output filenames will end in\
 \".ps\" \".gml\" \".svg\" \".ss\", respectively.\n\n"
string
typestr="ps|gml|xrna|svg"
default="ps"
optional

option  "pre"   -
"Add annotation macros to postscript file, and add the postscript code in \"string\" just\
 before the code to draw the structure. This is an easy way to add annotation.\n\n"
string
typestr="string"
optional

option  "post"  -
"Same as --pre but in contrast to adding the annotation macros. E.g to mark position\
 15 with circle use --post \"15 cmark\"\n\n"
string
typestr="string"
optional

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