package "Jnet"
# The version numbering scheme will be <major code revisions>.<updated training data>.<updated database/bug fixes>
version "2.2"
purpose "A consensus neural network protein secondary structure prediction method\n- Trained with SCOP 1.75 data and UniRef90 release 15.4"

# These are the data input parameters - only hmmer is required
option   "hmmer"        H  "HMMER profile"    string  typestr="filename"  required
option   "pssm"         p  "PSIBLAST PSSM"    string  typestr="filename"  optional

# Additional option for redirecting some output info into stderr
option "test" T  "Flag for test style output" flag off

# Program output, mutually exclusive
defgroup    "output"       groupdesc="Output options"
groupoption "concise"   -  "concise output (default)"   group="output"
groupoption "human"     -  "human readable output. Optionally, can take a width argument [default: 60]"   int   group="output" argoptional