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sleipnir / tools / SeekTest / SeekTest.ggo

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package	"SeekTest"
version	"1.0"
purpose	"Statistical test on a gene set for a given dataset"

section "Mode"
option	"dab"				D	"DAB mode"
								flag	off
option	"bin"				A	"PCL Bin mode"
								flag	off
option	"db"				d	"DB mode"
								flag 	off

section "DB mode"
option	"db_dir"			E	"DB directory"
								string typestr="directory"
option	"db_num"			b	"Number of files in DB directory"
								int default="1000"
option	"prep"				P	"Prep directory (containing .gavg and .gpres files)"
								string typestr="filename"
option	"sinfo"				s	"Sinfo directory (containing .sinfo files)"
								string typestr="filename"
option	"dataset_list"		C	"Dataset list"
								string typestr="filename"
option	"query"				Q	"List of genes separated by spaces in one line"
								string typestr="filename"
option	"quant"				q	"Quant file"
								string typestr="filename"
option	"count_pair"		c	"Count number of z-scores exceeding a threshold"
								flag	off
option	"histogram"			h	"Get distribution of z-scores of given genes"
								flag	off

section "DAB mode"
option	"gene_set_list"		g	"List of gene-set files"
								string typestr="filename"
option	"input"				x	"Gene mapping file"
								string typestr="filename"
option	"dabinput"			B	"DAB dataset file"
								string typestr="filename"
option 	"gavg_input"		a	"Gene average (.gavg) input file"
								string typestr="filename"
option 	"gpres_input"		p	"Gene presence (.gpres) input file"
								string typestr="filename"