sleipnir / tools / SVMhierarchy / SVMhierarchy.ggo

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package	"SVMhierarchy"
version	"1.0"
purpose	"Hierarchical Multilabel SVM powered by SVM-struct"

section "Main"
option	"labels"				l	"Labels file"
										string	typestr="filename"	no
option	"output"				o	"Output file "
										string	typestr="filename"  no
option	"input"					i	"Input PCL file "
										string	typestr="filename"  yes
option	"model"					m	"Model file"
										string	typestr="filename"  no
option	"ontoparam"				h	"Ontology file"
										string	typestr="filename"  no
option  "all"       			a   "Always classify all genes in PCLs"  
										flag off
option  "slack"       			S   "Use slack rescaling (NOT implemented for Hierarchical Multilabel SVM)"
										flag off

section "Options"
option "verbosity"  			v   "Sets the svm_struct verbosity"
										int default="0" no
option "skip"      				s   "Number of columns to skip in input pcls"
										int default="2" no
option	"normalize"				n	"Normalize PCLS to 0 mean 1 variance"
										flag	off
option	"cross_validation"		c	"Number of cross-validation sets ( arg of 1 will turn off cross-validation )"
										int default="5" no
option "loss_function" 		e   "Sets the loss function for SVM learning: Choice of:
0\tHamming distance loss: total number of differences in label vector.
1\tHamming distance loss (modified): total number of differences in label vector; over-annotation not counted as difference. 
2\tLikelihood distance loss. 
3\tLikelihood distance loss (modified). 
										int default="0" no
option "tradeoff"    			t   "SVM tradeoff constant C"
										float default="1" no
option "learning_algorithm" 		w   "Choice of structural learning algorithm (default 4):
0\tn-slack algorithm 
1\tn-slack algorithm with shrinking heuristic
2\t1-slack algorithm (primal) 
3\t1-slack algorithm (dual)
4\t1-slack algorithm (dual) with constraint cache\n" 
										int default="3" no
option	"threads"		p	"number of threads (only apply to algorithm 3 currently)"
										int default="4" no
option	"mmap"					M	"Memory map binary input"
										flag	off