--- /dev/null
+# Name of your program
+package "RNAplex" # don't use package if you're using automake
+purpose "Find targets of a query RNA"
+usage "RNAplex [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=RNAplex_cmdl --include-getopt --default-optional --func-name=RNAplex_cmdline_parser --arg-struct-name=RNAplex_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. Accessibility effects can be estimated by\
+ RNAplex if a RNAplfold accessibility profile is provided. The\
+ 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 "Input Options"
+sectiondesc="Below are command line options which alter the general input behavior of this program\n"
+
+option "query" q
+"File containing the query sequence.\n"
+details="Input sequences can be given piped to RNAplex or given in a query file with the -q option.\
+ Note that the -q option implies that the -t option is also used\n\n"
+string
+optional
+
+option "target" t
+"File containing the target sequence.\n"
+details="Input sequences can be given piped to RNAplex or given in a target file with the -t option.\
+ Note that the -t option implies that the -q option is also used\n\n"
+string
+optional
+
+option "accessibility-dir" a
+"Location of the accessibility profiles.\n"
+details="This option switches the accessibility modes on and indicates in which directory accessibility\
+ profiles as generated by RNAplfold can be found\n\n"
+string
+optional
+
+option "binary" b
+"Allow the reading and parsing of memory dumped opening energy file\n"
+details="The -b option allows to read and process opening energy files which are saved in binary format\n\
+ This can reduce by a factor of 500x-1000x the time needed to process those files. RNAplex recognizes the\
+ corresponding opening energy files by looking for files named after the sequence and containing the suffix\
+ _openen_bin. Please look at the man page of RNAplfold if you need more information on how to produce binary\
+ opening energy files.\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
+
+section "Algorithms"
+sectiondesc="Options which alter the computing behaviour of RNAplex.\n"
+
+# Options
+option "temp" T
+"Rescale energy parameters to a temperature T. Default is 37C.\n\n"
+double
+optional
+
+option "interaction-length" l
+"Maximal length of an interaction\n"
+details="Maximal allowed length of an interaction\n\n"
+default="40"
+int
+optional
+
+option "extension-cost" c
+"Cost to add to each nucleotide in a duplex\n"
+details="Cost of extending a duplex by one nucleotide. Allows to find compact duplexes, having few/small bulges or interior loops\
+ Only useful when no accessibility profiles are available. This option is disabled if accessibility profiles are used (-a option)\n\n"
+default="0"
+int
+optional
+
+option "probe-mode" p
+"Compute Tm for probes"
+details="Use this option if you want to compute the melting temperature of your probes\n\n"
+flag
+off
+
+option "probe-concentration" Q
+"Set the probe concentration for the Tm computation\n\n"
+double
+default="0.1"
+optional
+
+option "na-concentration" N
+"Set the Na+ concentration for the Tm computation\n\n"
+double
+default="1.0"
+optional
+
+option "mg-concentration" M
+"Set the Mg2+ concentration for the Tm computation\n\n"
+double
+default="1.0"
+optional
+
+option "k-concentration" K
+"Set the K+ concentration for the Tm computation\n\n"
+double
+default="1.0"
+optional
+
+option "tris-concentration" U
+"Set the tris+ concentration for the Tm computation\n\n"
+double
+default="1.0"
+optional
+
+
+
+
+
+
+
+option "fast-folding" f
+"Speedup of the target search\n"
+details="This option allows to decide if the backtracking has to be done (-f 0, -f 2) or not (-f 1). For -f 0 the structure is computed\
+ based on the standard energy model. This is the slowest and most precise mode of RNAplex. With -f 2, the structure is computed based on the approximated\
+ plex model. If a lot of targets are returned this is can greatly improve the runtime of RNAplex. -f 1 is the fastest mode, as no structure\
+ are recomputed \n\n"
+int
+default="0"
+optional
+
+option "scale-accessibility" V
+"Rescale all opening energy by a factor V\n"
+details="Scale-factor for the accessibility. If V is set to 1 then the scaling has no effect on the accessibility.\n\n"
+double
+default="1.0"
+optional
+
+option "constraint" C
+"Calculate structures subject to constraints.\n"
+details="The program reads first the\
+ sequence, then a string containing constraints on the structure for the query sequence encoded with the symbols:\n. (no constraint\
+ for this base)\n| (the corresponding base has to be paired)\n\n"
+flag
+off
+
+option "alignment-mode" A
+"Tells RNAplex to compute interactions based on alignments\n"
+details="If the A option is set RNAplex expects clustalw files as input for the -q and -t option.\n\n"
+flag
+off
+
+option "convert-to-bin" k
+"If set, RNAplex will convert all opening energy file in a directory set by the -a option into binary opening energy files\n"
+details="RNAplex can be used to convert existing text formatted opening energy files into binary formatted files. In this mode RNAplex does not compute interactions.\n\n"
+flag
+off
+
+section "Output"
+sectiondesc="Options that modify the output\n"
+
+option "duplex-distance" z
+"Distance between target 3' ends of two consecutive duplexes\n"
+details="Distance between the target 3'ends of two consecutive duplexes. Should be set to the maximal length of interaction to get\
+ good results\n\
+ Smaller z leads to larger overlaps between consecutive duplexes.\n\n"
+int
+default="0"
+optional
+
+option "energy-threshold" e
+"Minimal energy for a duplex to be returned\n"
+details="Energy threshold for a duplex to be returned. The threshold is set on the total energy of interaction, i.e. the hybridization\
+ energy corrected for opening energy if -a is set or the energy corrected by -c. If unset, only the mfe will be returned\n\n"
+double
+default="-100000"
+optional
+
+option "produce-ps" I
+"Draw an alignment annotated interaction from RNAplex\n"
+details="This option allows to produce interaction figures in PS-format a la RNAalifold, where base-pair conservation is represented in\
+ color-coded format. In this mode no interaction are computed, but the -I option indicates the location of the file containing interactions\
+ between two RNA (alignments/sequence) from a previous run. If the -A option is not set a structure figure a la RNAfold with color-coded annotation of the accessibilities is returned\n\n"
+string
+optional
+
+option "WindowLength" L
+"Tells how large the region around the target site should be for redrawing the alignment interaction\n"
+details="This option allow to specify how large the region surrounding the target site should be set when generating the alignment figure of the interaction\n\n"
+int
+default="1"
+optional
+
+
+text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n"
git://source.jalview.org / jabaws.git / blobdiff