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

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

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+# Name of your program
+package "RNAduplex" # don't use package if you're using automake
+purpose "Compute the structure upon hybridization of two RNA strands"
+#usage "RNAduplex [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=RNAduplex_cmdl --include-getopt --default-optional --func-name=RNAduplex_cmdline_parser --arg-struct-name=RNAduplex_args_info"
+
+
+description "reads two RNA sequences from stdin or <filename> and computes optimal\
+ and suboptimal secondary structures for their hybridization. The calculation is simplified\
+ by allowing only inter-molecular base pairs, for the general case use RNAcofold.\nThe computed\
+ optimal and suboptimal structure are written to stdout, one structure per line. Each line consist\
+ of: The structure in dot bracket format with a \"&\" separating the two strands. The range of the\
+ structure in the two sequences in the format  \"from,to : from,to\"; the energy of duplex structure\
+ in kcal/mol.\nThe format is especially useful for computing the hybrid structure between a small\
+ probe sequence and a long target sequence.\n"
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n"
+
+option  "sorted"  s
+"sort the printed output by free energy\n\n"
+flag
+off
+
+option  "noconv"  -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+section "Algorithms"
+sectiondesc="Select additional algorithms which should be included in the calculations.\n"
+
+option  "deltaEnergy" e
+"Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol).\
+ Default is calculation of mfe structure only.\n\n"
+float
+typestr="range"
+optional
+
+section "Model Details"
+
+option  "temp"  T
+"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
+double
+optional
+
+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 is the\
+ default for mfe folding but 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\
+ and works only for mfe folding.\n\nNote that by default (as well as with -d1 and -d3) pf and mfe folding\
+ treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same\
+ energy model.\n\n"
+int
+default="2"
+optional
+
+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  "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  "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
+optional
+hidden
+
+text    "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"