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

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

diff --git a/binaries/src/ViennaRNA/Progs/RNAeval.ggo b/binaries/src/ViennaRNA/Progs/RNAeval.ggo
new file mode 100644 (file)
index 0000000..8c49c02
--- /dev/null
+++ b/binaries/src/ViennaRNA/Progs/RNAeval.ggo
@@ -0,0 +1,91 @@
+# Name of your program
+package "RNAeval" # don't use package if you're using automake
+purpose "calculate energy of RNA sequences with given secondary structure"
+#usage "RNAeval [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=RNAeval_cmdl --include-getopt --default-optional --func-name=RNAeval_cmdline_parser --arg-struct-name=RNAeval_args_info"
+
+
+description "Evaluates the free energy of an RNA molecule in fixed secondary structure.\
+ Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written\
+ to stdout.\nThe program will continue to read new sequences and structures until a line\
+ consisting of the single character \"@\" or an end of file condition is encountered.\nIf\
+ the input sequence or structure contains the separator character \"&\" the program calculates\
+ the energy of the co-folding of two RNA strands, where the \"&\" marks the boundary between\
+ the two strands.\n"
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option  "noconv"  -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+option "verbose" v
+"Print out energy contribution of each loop in the structure.\n\n"
+flag
+off
+
+section "Model Details"
+
+option  "temp"  T
+"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
+double
+
+option  "noTetra" 4
+"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
+flag
+off
+
+option  "dangles" d
+"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
+details="\nWith -d1 only unpaired bases can participate in at most one dangling end, this unsupported for the\
+ partition function folding.\n\nWith -d2 this check is ignored,\
+ dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the\
+ default for partition function folding (-p).\nThe option -d0 ignores dangling ends altogether (mostly for\
+ debugging).\nWith -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the\
+ moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3.\n"
+int
+default="2"
+optional
+
+option  "energyModel" e
+"Rarely used option to fold sequences from the artificial ABCD... alphabet, where\
+ A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.\n\n"
+int
+optional
+
+option  "paramFile" P
+"Read energy parameters from paramfile, instead of using the default parameter set.\n"
+details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
+ documentation for details on the file format.\n\n"
+string
+typestr="paramfile"
+optional
+
+option  "circ" c
+"Assume a circular (instead of linear) RNA molecule.\n\n"
+flag
+off
+
+option  "gquad" g
+"Incoorporate G-Quadruplex formation into the structure prediction algorithm\n"
+flag
+off
+
+option  "logML" -
+"Recalculate energies of structures using a logarithmic energy function for multi-loops before output.\n"
+details="This option does not effect structure generation, only the energies that are printed out.\
+ Since logML lowers energies somewhat, some structures may be missing.\n\n"
+flag
+off
+
+text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"