Source

sleipnir / tools / Dat2Dab / Dat2Dab.ggo

package	"Dat2Dab"
version	"1.0"
purpose	"Text/binary data file interconversion"

section "Main"
option	"input"			i	"Input DAT/DAB file"
							string	typestr="filename"
option	"output"		o	"Output DAT/DAB file"
							string	typestr="filename"
option	"quant"			q	"Input Quant file"
							string	typestr="filename"

section "Preprocessing"
option	"flip"			f	"Calculate one minus values"
							flag	off
option	"abs"			B	"Calculate absolute values"
							flag	off
option	"normalize"		n	"Normalize to the range [0,1]"
							flag	off
option	"normalizeNPone"	w	"Normalize to the range [-1,1]"
							flag	off
option	"normalizeDeg"		j	"Normalize by incident node degrees"
							flag	off
option	"normalizeLoc"		k	"Normalize by local neighborhood"
							flag	off
option	"zscore"		z	"Convert values to z-scores"
							flag	off
option	"rank"			r	"Rank transform data"
							flag	off
option	"randomize"		a	"Randomize data"
							flag	off
option	"NegExp"		K	"Transform all values to their negative exponential (converts -log of prob back to prob space)"
							flag	off

section "Filtering"
option	"genes"			g	"Process only genes from the given set"
							string	typestr="filename"
option	"genex"			G	"Exclude all genes from the given set"
							string	typestr="filename"
option	"genee"			D	"Process only edges including a gene from the given set"
							string	typestr="filename"
option	"edges"			e	"Process only edges from the given DAT/DAB"
							string	typestr="filename"
option	"exedges"		x	"Exclude edges from the given DAT/DAB"
							string	typestr="filename"
option	"gexedges"		X	"Exclude all edges which both genes from the given set"
							string	typestr="filename"
option	"cutoff"		c	"Exclude edges below cutoff"
							double
option	"zero"			Z	"Zero missing values"
							flag	off
option	"dval"			V	"set all non-missing values to a set default value"
							float	
option	"dmissing"		M	"set missing values to a set default value"
							float	
option	"duplicates"		d	"Allow dissimilar duplicate values"
							flag	off
option	"subsample"		u	"Fraction of output to randomly subsample"
							float	default="1"

section "Lookups"
option	"lookup1"		l	"First lookup gene"
							string
option	"lookup2"		L	"Second lookup gene"
							string
option	"lookups1"		t	"First lookup gene set"
							string	typestr="filename"
option	"lookups2"		T	"First lookup gene set"
							string	typestr="filename"
option	"genelist"		E	"Only list genes"
							flag	off
option	"paircount"		P	"Only count pairs above cutoff"
							flag	off
option	"ccoeff"		C	"Output clustering coefficient for each gene"
							flag	off
option	"hubbiness"		H	"Output the average edge weight for each gene"
							flag	off
option	"mar"			J	"Output the maximum adjacency ratio for each gene"
							flag	off

section "Optional"
option	"remap"			p	"Gene name remapping file"
							string	typestr="filename"
option	"table"			b	"Produce table formatted output"
							flag	off
option	"skip"			s	"Columns to skip in input PCL"
							int	default="2"
option	"memmap"		m	"Memory map input/output"
							flag	off
option	"random"		R	"Seed random generator (default -1 uses current time)"
							int	default="-1"
option	"noise"			N	"Add noise from standard Normal to all non-missing values"
							flag	off
option	"verbosity"		v	"Message verbosity"
							int	default="5"