load_package %L/cap3	{}	cap3	0

set_menu	gap_menu
add_menu	Assembly	1 2 left
set fs ""
catch {set fs [open "|cap3_s" r]}
if {$fs == ""} {
    add_cascade	{Assembly.CAP3 Assembly} 0 0
} else {
    catch {close $fs}
    add_cascade	{Assembly.CAP3 Assembly} 12 22
}
add_command	{Assembly.CAP3 Assembly.Perform CAP3 assembly} \
			12 22 {HuangAssembly_3 \$io 1}
add_command	{Assembly.CAP3 Assembly.Import CAP3 assembly data} \
			12 22 {HuangImport_3 \$io}
add_command	{Assembly.CAP3 Assembly.Perform and import CAP3 assembly} \
			12 22 {HuangAssembly_3 \$io 2}

set_defx defs_f_or_l_in	WHICH.NAME	"Input from"
set_defx defs_f_or_l_in	WHICH.BUTTONS	{list file}
set_defx defs_f_or_l_in	WHICH.VALUE	2
set_defx defs_f_or_l_in	NAME.NAME	"List or file name"
set_defx defs_f_or_l_in	NAME.BROWSE	"Browse"
set_defx defs_f_or_l_in	NAME.VALUE	""

set_defx defs_f_or_l_out	WHICH.NAME	"Output to"
set_defx defs_f_or_l_out	WHICH.BUTTONS	{list file}
set_defx defs_f_or_l_out	WHICH.VALUE	2
set_defx defs_f_or_l_out	NAME.NAME	"List or file name"
set_defx defs_f_or_l_out	NAME.BROWSE	"Browse"
set_defx defs_f_or_l_out	NAME.VALUE	""

set_def HUANG_ASSEMBLY1.WIN     .cap3_perform_assembly
set_def HUANG_ASSEMBLY2.WIN     .cap3_import_assembly
set_def HUANG_ASSEMBLY3.WIN     .cap3_perform_import_assembly

set_def HUANG_ASSEMBLY.INFILE                   $defs_f_or_l_in
set_def HUANG_ASSEMBLY.INFILE.WHICH.NAME        "Input readings from"
set_def HUANG_ASSEMBLY.CONS.NAME		"Use constraint file"
set_def HUANG_ASSEMBLY.CONS.VALUE		0
set_def HUANG_ASSEMBLY.DEST.NAME                "Destination directory"
set_def HUANG_ASSEMBLY.DEST.VALUE               "assemble"
set_def HUANG_ASSEMBLY.FORMAT.NAME              "Input reading format"
set_def HUANG_ASSEMBLY.FORMAT.VALUE             1
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.1          "experiment"
set_def HUANG_ASSEMBLY.FORMAT.BUTTON.2          "fasta"
set_def HUANG_ASSEMBLY.OUTFILE                  $defs_f_or_l_out
set_def HUANG_ASSEMBLY.OUTFILE.WHICH.NAME       "Save failures to"
set_def HUANG_ASSEMBLY.INDIR.NAME               "Directory containing assembled readings"
set_def HUANG_ASSEMBLY.FOFN                     "fofn"

set_def HUANG_ASSEMBLY.BAND_EXP.NAME	"Band expansion size"
set_def HUANG_ASSEMBLY.BAND_EXP.VALUE	20
set_def HUANG_ASSEMBLY.BAND_EXP.MIN	10

set_def HUANG_ASSEMBLY.QUAL_DIFF.NAME	"Base quality cutoff for differences"
set_def HUANG_ASSEMBLY.QUAL_DIFF.VALUE 	20	
set_def HUANG_ASSEMBLY.QUAL_DIFF.MIN	16
set_def HUANG_ASSEMBLY.QUAL_DIFF.MAX	99

set_def HUANG_ASSEMBLY.QUAL_CLIP.NAME	"Base quality cutoff for clipping"
set_def HUANG_ASSEMBLY.QUAL_CLIP.VALUE 	10	
set_def HUANG_ASSEMBLY.QUAL_CLIP.MIN	6
set_def HUANG_ASSEMBLY.QUAL_CLIP.MAX	99

set_def HUANG_ASSEMBLY.QSCORE.NAME 	"Max qscore sum at differences"
set_def HUANG_ASSEMBLY.QSCORE.VALUE	200
set_def HUANG_ASSEMBLY.QSCORE.MIN	100

set_def HUANG_ASSEMBLY.CLEARANCE.NAME	"Clearance between no. of diff"
set_def HUANG_ASSEMBLY.CLEARANCE.VALUE	30
set_def HUANG_ASSEMBLY.CLEARANCE.MIN	10

set_def HUANG_ASSEMBLY.GAP_PENALTY.NAME		"Gap penalty factor"
set_def HUANG_ASSEMBLY.GAP_PENALTY.VALUE	6
set_def HUANG_ASSEMBLY.GAP_PENALTY.MIN		0

set_def HUANG_ASSEMBLY.MATCH_SCORE.NAME		"Match score factor"
set_def HUANG_ASSEMBLY.MATCH_SCORE.VALUE	2
set_def HUANG_ASSEMBLY.MATCH_SCORE.MIN		0

set_def HUANG_ASSEMBLY.MISMATCH_SCORE.NAME	"Mismatch score factor"
set_def HUANG_ASSEMBLY.MISMATCH_SCORE.VALUE	-5
set_def HUANG_ASSEMBLY.MISMATCH_SCORE.MAX	0

set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.NAME	"Overlap length cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.VALUE	30
set_def HUANG_ASSEMBLY.OVERLAP_LENGTH.MIN	20

set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.NAME	"Overlap percent identity cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.VALUE	75
set_def HUANG_ASSEMBLY.OVERLAP_IDENTITY.MIN	65

set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.NAME	"Overlap similarity score cutoff"
set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.VALUE	500
set_def HUANG_ASSEMBLY.OVERLAP_SIMILARITY.MIN	100

set_def HUANG_ASSEMBLY.MIN_CORRECTION.NAME	"Min number of constraints for correction"
set_def HUANG_ASSEMBLY.MIN_CORRECTION.VALUE	4
set_def HUANG_ASSEMBLY.MIN_CORRECTION.MIN	0

set_def HUANG_ASSEMBLY.MIN_LINKING.NAME	"Min number of constraints for linking"
set_def HUANG_ASSEMBLY.MIN_LINKING.VALUE	2
set_def HUANG_ASSEMBLY.MIN_LINKING.MIN	0

set_def HUANG_ASSEMBLY.PREFIX.NAME	"Prefix string for output file names"
set_def HUANG_ASSEMBLY.PREFIX.VALUE	cap

