# -*-Perl-*- 
#
# Config file for finish -- DMH 
#
#
#
#
    $params = {

	'project' => {
	    'type' => 'text',
	    'value' => 'none',
	    'label' => 'Project',		
	},
		
	'version' => {
	    'type' => 'text',
	    'value' => 0,
	    'label' => 'Version'
	},
		
		
	'project_dir' => {
	    'type' => 'text',
	    'value' => $ENV{'PWD'},
	    'label' => 'Project Directory'
	},
		
	'output_dir' => {
	    'type' => 'text',
	    'value' => $ENV{'PWD'},,
	    'label' => 'Output directory'
	},
		
	'short_file' => {
	    'type' => 'text',
	    'value' => "finish.short",
	    'label' => 'Short output filename'
	},
		 
	'long_file' => {
	    'type' => 'text',
	    'value' => "finish.long",
	    'label' => 'Long ouput filename'
	},

	'autoselect' => {
	    'type' => 'singlechoice',
	    'value' => 1,
	    'label' => 'Autoselect all reactions',
	    'options' => {
		'Yes' => 1,
		'No' => 0
		}
	},

	'distribution' => {
	    'type' => 'singlechoice',
	    'value' => 'u',
	    'label' => 'Distribution',
	    'options' => {
		'Uniform' => 'u',
		'Custom File' => 'd'
		}
	},

	'operation' => {
	    'type' => 'singlechoice',
	    'label' => 'Finish mode',
	    'value' => 'b',
	    'options' => {
		'Double stand' => 'd',
		'Extend' => 'e',
		'Both' => 'b',
		}
	},

	'emode' => {
	    'type' => 'multichoice',
	    'label' => 'Read types for extension',
	    'options' => {
		'long' => 1,
		'reverse' => 1,
		'terminator' => 0,
		'oligo' => 1
		}
	},

	'dsmode' => {
	    'type' => 'multichoice',
	    'label' => 'Read types for double-stranding',
	    'options' => {
		'long' => 0,
		'reverse' => 0,
		'terminator' => 1,
		'oligo' => 0
		}
	},

	'cost_xl' => {
	    'type' => 'range',
	    'label' => 'Relative cost of a long read',
	    'value' => 1.0,
	    'default' => 1.0,
	    'from' => 0,
	    'to' => 20,
	    'tick' => 5,
	    'resolution' => '.2'
	},

	'cost_rv' => {
	    'type' => 'range',
	    'label' => 'Relative cost of a reverse read',
	    'value' => 2.2,
	    'default' => 2.2,
	    'from' => 0,
	    'to' => 20,
	    'tick' => 5,
	    'resolution' => '.2'
	},

	'cost_tm' => {
	    'type' => 'range',
	    'label' => 'Relative cost of a terminator read',
	    'value' => 2.0,
	    'default' => 2.0,
	    'from' => 0,
	    'to' => 20,
	    'tick' => 5,
	    'resolution' => '.2'
	},
	
	'cost_fo' => {
	    'type' => 'range',
	    'label' => 'Relative cost of a forward oligo',
	    'value' => 9.0,
	    'default' => 9.0,
	    'from' => 0,
	    'to' => 20,
	    'tick' => 5,
	    'resolution' => '.2'
	},
		
	'cost_ro' => {
	    'type' => 'range',
	    'label' => 'Relative cost of a reverse oligo',
	    'value' => 9.0,
	    'default' => 9.0,
	    'from' => 0,
	    'to' => 20,
	    'tick' => 5,
	    'resolution' => '.2'
	},

	'min_contig' => {
	    'type' => 'range',
	    'label' => 'Minimum contig length to finish',
	    'value' => 750,
	    'default' => 750,
	    'from' => 0,
	    'to' => 10000,
	    'tick' => 2000,
	    'resolution' => '10'
	},

	'min_ss_region' => {
	    'type' => 'range',
	    'label' => 'Minimum single stranded region to finish',
	    'value' => 50,
	    'default' => 50,
	    'from' => 0,
	    'to' => 1000,
	    'tick' => 200,
	    'resolution' => '5'
	},

	'min_added_cov' => {
	    'type' => 'range',
	    'label' => 'Minimum contribution of new bases',
	    'value' => 20,
	    'default' => 20,
	    'from' => 0,
	    'to' => 200,
	    'tick' => 20,
	    'resolution' => '1'
	},

	'min_prob' => {
	    'type' => 'range',
	    'label' => 'Probability threshold',
	    'value' => 0.5,
	    'default' => 0.5,
	    'from' => 0,
	    'to' => 1,
	    'tick' => 0.1,
	    'resolution' => '0.1'
	},



    };
