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

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

diff --git a/binaries/src/ViennaRNA/Progs/RNAparconv.ggo b/binaries/src/ViennaRNA/Progs/RNAparconv.ggo
new file mode 100644 (file)
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--- /dev/null
+++ b/binaries/src/ViennaRNA/Progs/RNAparconv.ggo
@@ -0,0 +1,123 @@
+# 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  "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  "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  "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"