WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / Progs / RNAplot.ggo

diff --git a/binaries/src/ViennaRNA/Progs/RNAplot.ggo b/binaries/src/ViennaRNA/Progs/RNAplot.ggo
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/Progs/RNAplot.ggo
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+# 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"