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

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

diff --git a/binaries/src/ViennaRNA/Progs/RNAPKplex.ggo b/binaries/src/ViennaRNA/Progs/RNAPKplex.ggo
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+# Name of your program
+package "RNAPKplex" # don't use package if you're using automake
+purpose "predicts RNA secondary structures including pseudoknots"
+#usage "PKplex [options]\n"
+
+# Version of your program
+#version "0.1"   # don't use version if you're using automake
+
+
+# command line options passed to gengetopt
+args "--file-name=RNAPKplex_cmdl --include-getopt --default-optional --func-name=PKplex_cmdline_parser --arg-struct-name=PKplex_args_info"
+
+
+description "Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using\
+ the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm\
+ uses O(n^2*w^4) CPU time and O(n*w^2) memory space.\nThe algorithm furthermore always considers dangle=2 model.\n"
+
+# Options
+option  "cutoff"  c
+"Report only base pairs with an average probability > cutoff in the dot plot\n\n"
+float
+default="0.01"
+optional
+
+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 stabilizing energies for certain tetra-loops. Mostly for testing.\n\n"
+flag
+off
+
+option  "noLP"  -
+"Produce structures without lonely pairs (helices of length 1).\n"
+details="For partition function folding this only disallows pairs that can only occur isolated. Other\
+ pairs may still occasionally occur as helices of length 1.\n\n"
+flag
+off
+
+option  "noGU"  -
+"Do not allow GU pairs\n\n"
+flag
+off
+
+option  "noClosingGU" -
+"Do not allow GU pairs at the end of helices\n\n"
+flag
+off
+
+option  "noconv"  -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+option  "nsp" -
+"Allow other pairs in addition to the usual AU,GC,and GU pairs.\n"
+details="Its argument is a comma separated list of additionally allowed pairs. If the\
+ first character is a \"-\" then AB will imply that AB and BA are allowed pairs.\ne.g.\
+ RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking\
+ energy.\n\n"
+string
+default="empty"
+optional
+
+option  "energyCutoff" e
+"Energy cutoff or pseudoknot initiation cost. Minimum energy gain of a pseudoknot\
+ interaction for it to be returned. Pseudoknots with smaller energy gains are\
+ rejected.\n\n"
+double
+default="-8.10"
+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 "verbose" v
+"print verbose output\n"
+flag
+off
+
+option "subopts" s
+"print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is smaller than the given value.\n"
+details="NOTE: The final energy of a structure is calculated as the sum\
+ of the pseudoknot interaction energy, the penalty for initiating\
+ a  pseudoknot and the energy of the pseudoknot-free part of the\
+ structure. The -s option only takes the pseudoknot interaction\
+ energy into account, so the final energy differences may be bigger\
+ than the specified value (default=0.).\n\n"
+double
+default="0.0"
+optional
+
+text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"
+