Source

sleipnir / tools / SeekReader / SeekReader.ggo

package	"SeekReader"
version	"1.0"
purpose	"Reads db files"

section "Diagnosis"
option	"databaselet"		D	"Display values from databaselet(s)"
								flag	off
option	"dataset"			A	"Check which datasets contain query of interest, based on .gpres file"
								flag	off
option	"weight"			W	"Test dataset weights"
								flag	off
option	"weight2"			U	"Test dataset weights 2"
								flag	off
option	"comp_ranking"		C	"Compare two rankings (*.gscore files)"
								flag	off
option	"convert_aracne"	J	"Convert Aracne output (.txt) to DAB file"
								flag	off
option	"limit_hub"			Y	"Limit genes in the DAB to those that are hubby"
								flag	off

section "Limit Hub"
option	"dabinput"			y	"DAB input file"
								string typestr="filename" default="NA"
option	"hub_dab_output"	Z	"DAB output file"
								string typestr="filename" default="NA"

section	"Convert Aracne"
option	"aracne_file"		K	"Aracne .txt output file"
								string typestr="filename" default="NA"
option	"output_dab_file"	L	"DAB file"
								string typestr="filename" default="NA"

section "Weight"
option	"dweight_dir"		E	"Dataset weight directory"
								string typestr="directory" default="NA"
option	"dweight_num"		n	"Number of .dweight files"
								int	default="1000"
option	"dweight_map"		M	"Dataset mapping file"
								string typestr="filename" default="NA"
option	"dweight_test_dir"	F	"Test dataset weight directory"
								string typestr="directory" default="NA"
option	"dweight_test_num"	G	"Test number of .dweight files"
								int	default="1000"

section "Compare Rankings"
option	"gscore_dir1"		H	"Gene score directory 1"
								string typestr="directory" default="NA"	
option	"gscore_dir2"		h	"Gene score directory 2"	
								string typestr="directory" default="NA"	
option	"gscore_num1"		I	"Number of .gscore files"
								int default="1000"


section "Main"
option	"order_stat_single_gene_query"		O	"Order statistics mode (single-gene query)"
								flag	off
option	"db"				x	"Input dataset-platform definition"
								string	typestr="filename"
option	"dset_list"			X	"Input a set of datasets"
								string	typestr="filename"
option	"input"				i	"Input gene mapping"
								string	typestr="filename"
option	"single_query"		q	"Query gene list"
								string	typestr="filename"
option	"dir_in"			d	"Database directory"
								string	typestr="directory"
option	"dir_prep_in"		p	"Prep directory (containing .gavg, .gpres files)"
								string	typestr="directory"				
option	"dir_gvar_in"		r	"Prep directory (containing .gexpvar files)"
								string	typestr="directory"	default="NA"	
option	"dir_sinfo_in"		s	"Sinfo directory (containing .sinfo files)"
								string	typestr="directory"	default="NA"
option	"is_nibble"			N	"Whether the input DB is nibble type"
								flag	off
option	"platform_dir"		P	"Platform directory"
								string	typestr="directory"
option	"gvar_cutoff"		v	"Query gene's variance in the dataset cutoff"
								float	default="-1"
option	"multi_query"		Q	"File containing multiple queries"
								string	typestr="filename"	default="NA"
option	"output_file"		o	"Output file"
								string	typestr="filename"	default="NA"
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
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Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.