--- /dev/null
+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