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sleipnir / tools / SeekIterative / SeekIterative.ggo

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package	"SeekIterative"
version	"1.0"
purpose	"Search based on iterative algorithm"

section "Mode"
option	"dab"				d	"Sparse Dab mode"
								flag off
option	"combined"			e	"Combined-dab mode"
								flag off
option	"test"				f	"Test mode"
								flag off
option	"testcount"			g	"Test count mode"
								flag off
option	"testcombined"		h	"Test count mode"
								flag off
option	"visualize"			v	"Visualization mode"
								flag off

section "Combined-DAB / Visualization mode"
option	"dab_basename"		b	"Combined-dab basename, also shared with Test Mode"
								string typestr="filename"

section "Visualization mode"
option	"cutoff"			c	"Cutoff value"
								float default="0.0001"
option	"genome"			G	"Genome mapping file"
								string typestr="filename"

section "Sparse DAB mode"
option	"dab_list"			V	"DAB list"
								string typestr="filename"
option	"num_iter"			I	"Number of iterations"
								int	default="0"
option	"default_type"		T	"Default gene index type (choose unsigned short for genes, or unsigned int (32-bit) for transcripts) (required for DAB mode) (0 - unsigned int, 1 - unsigned short)"
								int default="-1"
option	"rbp_p"				R	"RBP p parameter (must be specified) (p<1.0) (recommended > 0.95)"
								float default="-1"
option	"max_rank"			M	"Maximum rank number in the sparse DAB matrix (must be specified)"
								int default="-1"

section "Input"
option	"input"				i	"Gene mapping file"
								string typestr="filename"	yes
option	"query"				q	"Query file"
								string typestr="filename"	yes
option	"dab_dir"			F	"DAB directory"
								string typestr="directory"	yes

section "Output"
option	"dir_out"			D	"Output directory"
								string typestr="directory"