JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / jnet / cmdline / cmdline.ggo

diff --git a/sources/jnet/cmdline/cmdline.ggo b/sources/jnet/cmdline/cmdline.ggo
new file mode 100644 (file)
index 0000000..c3fa853
--- /dev/null
+++ b/sources/jnet/cmdline/cmdline.ggo
@@ -0,0 +1,16 @@
+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