sleipnir / tools / SeekServer / SeekServer.ggo

package	"SeekServer"
version	"1.0"
purpose	"Performs cross-platform microarray query-guided search in server mode"

section "Main"
option	"port"				t	"Port"
								string default="9000"	yes
option	"dset"				x	"Input a set of datasets"
								string typestr="filename"	yes
option	"input"				i	"Input gene mapping"
								string	typestr="filename"	yes
option	"dir_in"			d	"Database directory"
								string	typestr="directory"	yes
option	"dir_prep_in"		p	"Prep directory (containing .gavg, .gpres files)"
								string	typestr="directory"	yes
option	"dir_platform"		P	"Platform directory (containing .gplatavg, .gplatstdev, .gplatorder files)"
								string	typestr="directory"	yes
option	"dir_sinfo"			u	"Sinfo Directory (containing .sinfo files)"
								string	typestr="directory"	default="NA"	yes
option	"dir_gvar"			U	"Gene variance directory (containing .gexpvar files)"
								string	typestr="directory"	default="NA"
option	"quant"				Q	"quant file (assuming all datasets use the same quantization)"
								string	typestr="filename"	yes								
option	"num_db"			n	"Number of databaselets in database"
								int	default="1000"	yes

section "Optional - Parameter tweaking"
option	"score_cutoff"		c	"Cutoff on the gene-gene score before adding, default: no cutoff"
								float default="-9999"
option	"per_q_required"	C	"Fraction (max 1.0) of query required to correlate with a gene, in order to count the gene's query score. A gene may not correlate with a query gene if it is absent, or its correlation with query does not pass cut-off (specified by --score_cutoff). Use this with caution. Be careful if using with --score_cutoff."
								float default="0.0"
option	"square_z"			e	"If using z-score, square-transform z-scores. Usually used in conjunction with --score-cutoff"							
								flag	off

section "MISC"								
option	"is_nibble"			N	"If true, the input DB is nibble type"
								flag	off
option	"buffer"			b	"Number of Databaselets to store in memory"
								int default="20"
option	"output_text"		O	"Output results (gene list and dataset weights) as text"
								flag	off
option	"additional_db"		B	"Utilize a second CDatabase collection. Path to the second CDatabase's setting file."
								string default="NA"