X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=sources%2Fjnet%2Fcmdline%2Fcmdline.ggo;fp=sources%2Fjnet%2Fcmdline%2Fcmdline.ggo;h=c3fa8539b7aa2c896267e849badfc9f915f8d595;hb=81362e35a140cd040e948b921053e74267f8a6e3;hp=0000000000000000000000000000000000000000;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

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+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