tool_settings	bed_wb_import	run_on_cluster	true
tool_settings	bed_wb_import	tmp_directory	tmp
tool_settings	bed_wb_import	use_cache	true
tool_settings	bed_wb_import	wait_for_cluster	true
tool_settings	blast	blast_db_dir	/www/blastdb/biocomp/moderated/plaza/
tool_settings	blast	blast_db_genomes_dir	/www/blastdb/biocomp/moderated/plaza/public_05/
tool_settings	blast	blast_db_genomes_prefix	plaza_genomes_public_05
tool_settings	blast	blast_db_proteins	plaza_proteins_public_dicots_05
tool_settings	blast	blast_db_transcripts	plaza_transcripts_public_dicots_05
tool_settings	blast	cluster_max_runtime	300
tool_settings	blast	cluster_queue	medium
tool_settings	blast	default_evalue	1e-5
tool_settings	blast	possible_evalues	1e-10;1e-5;0.001;0.1;1;10
tool_settings	blast	run_on_cluster	true
tool_settings	blast	tmp_directory	blast
tool_settings	blast	wait_for_cluster	true
tool_settings	blastdbcmd	blast_db_genomes_dir	/www/blastdb/biocomp/moderated/plaza/public_05/
tool_settings	blastdbcmd	blast_db_genomes_prefix	plaza_genomes_public_05
tool_settings	blastdbcmd	run_on_cluster	false
tool_settings	blastdbcmd	tmp_directory	blast
tool_settings	blastdbcmd	use_cache	false
tool_settings	blastdbcmd	wait_for_cluster	true
tool_settings	blast_ncbi	time_out	60
tool_settings	blast_ncbi	tmp_directory	blast_ncbi
tool_settings	blast_wb_import	blast_db_dir	/www/blastdb/biocomp/moderated/plaza/
tool_settings	blast_wb_import	blast_db_proteins	plaza_proteins_public_dicots_05
tool_settings	blast_wb_import	blast_db_transcripts	plaza_transcripts_public_dicots_05
tool_settings	blast_wb_import	cluster_queue	long
tool_settings	blast_wb_import	default_evalue	1e-5
tool_settings	blast_wb_import	possible_evalues	1e-10;1e-5;0.001;0.1;1;10
tool_settings	blast_wb_import	run_on_cluster	true
tool_settings	blast_wb_import	tmp_directory	blast
tool_settings	blast_wb_import	use_cache	false
tool_settings	blast_wb_import	wait_for_cluster	false
tool_settings	enrichment	cluster_interval_check	10
tool_settings	enrichment	default_evalue	0.05
tool_settings	enrichment	possible_evalues	0.05;0.01;0.005;0.001
tool_settings	enrichment	run_on_cluster	true
tool_settings	enrichment	tmp_directory	workbench
tool_settings	enrichment	use_cache	true
tool_settings	enrichment	wait_for_cluster	true
tool_settings	expansion_plot	default_drawing_size	50
tool_settings	expansion_plot	possible_drawing_sizes	50;100
tool_settings	functional_cluster	run_on_cluster	false
tool_settings	functional_cluster	tmp_directory	functional_clustering
tool_settings	functional_cluster	use_cache	true
tool_settings	functional_cluster	wait_for_cluster	false
tool_settings	gene_structure	run_on_cluster	false
tool_settings	gene_structure	tmp_directory	gene_structure
tool_settings	gene_structure	use_cache	true
tool_settings	gene_structure	wait_for_cluster	false
tool_settings	gf_finder_enriched	default_expansion_ratio	2
tool_settings	gf_finder_enriched	default_maximum_gf_size	500+
tool_settings	gf_finder_enriched	default_minimum_gf_size	20
tool_settings	gf_finder_enriched	possible_expansion_ratios	2:2x;5:5x;10:10x;20:20x
tool_settings	gf_finder_enriched	possible_maximum_gf_sizes	2;5;10;20;50;100;200;500;500+
tool_settings	gf_finder_enriched	possible_minimum_gf_sizes	2;5;10;20;50;100;200;500
tool_settings	gf_finder_specific	default_max_gf_size	500+
tool_settings	gf_finder_specific	default_min_gf_size	2
tool_settings	gf_finder_specific	possible_max_gf_sizes	2;5;10;20;50;100;200;500;500+
tool_settings	gf_finder_specific	possible_min_gf_sizes	2;5;10;20;50;100;200;500;500+
tool_settings	gf_heatmap	max_genes	100
tool_settings	go_enrichment	cluster_interval_check	10
tool_settings	go_enrichment	cluster_max_runtime	300
tool_settings	go_enrichment	default_evalue	0.05
tool_settings	go_enrichment	possible_evalues	0.05;0.01;0.005;0.001
tool_settings	go_enrichment	run_on_cluster	true
tool_settings	go_enrichment	tmp_directory	go_enrichment
tool_settings	go_enrichment	use_cache	true
tool_settings	go_enrichment	wait_for_cluster	true
tool_settings	igv.js	annotation_directory	GFF/%SPECIES%/
tool_settings	igv.js	annotation_file_compressed	true
tool_settings	igv.js	annotation_file_extension	gff3
tool_settings	igv.js	annotation_file_prefix	annotation.all_transcripts.all_features
tool_settings	igv.js	data_url	https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/
tool_settings	igv.js	genomes_directory	Genomes
tool_settings	igv.js	genomes_file_compressed	true
tool_settings	igv.js	genomes_file_extension	fasta
tool_settings	interactive_phylogenetics_module	allow_asynchronous_use	true
tool_settings	interactive_phylogenetics_module	cluster_interval_check	10
tool_settings	interactive_phylogenetics_module	cluster_max_runtime	300
tool_settings	interactive_phylogenetics_module	cluster_queue	medium
tool_settings	interactive_phylogenetics_module	run_on_cluster	true
tool_settings	interactive_phylogenetics_module	tmp_directory	analysis
tool_settings	interactive_phylogenetics_module	use_cache	true
tool_settings	interactive_phylogenetics_module	wait_for_cluster	true
tool_settings	msa	tmp_directory	msa
tool_settings	multiplicon	run_on_cluster	false
tool_settings	multiplicon	tmp_directory	multiplicon
tool_settings	multiplicon	use_cache	true
tool_settings	multiplicon	wait_for_cluster	false
tool_settings	phylogenetic_tree	run_on_cluster	false
tool_settings	phylogenetic_tree	tmp_directory	atv
tool_settings	phylogenetic_tree	use_cache	true
tool_settings	phylogenetic_tree	wait_for_cluster	false
tool_settings	skyline	default_window_size	200
tool_settings	skyline	possible_window_sizes	-1:Whole chromosome;50;100;200;500
tool_settings	skyline	run_on_cluster	false
tool_settings	skyline	tmp_directory	skyline
tool_settings	skyline	use_cache	true
tool_settings	skyline	wait_for_cluster	true
tool_settings	synteny	default_window_size	5
tool_settings	synteny	possible_window_sizes	5;10;15
tool_settings	synteny	run_on_cluster	false
tool_settings	synteny	tmp_directory	synteny
tool_settings	synteny	use_cache	true
tool_settings	synteny	wait_for_cluster	false
tool_settings	wb_functional_stats	run_on_cluster	false
tool_settings	wb_functional_stats	tmp_directory	workbench
tool_settings	wb_functional_stats	wait_for_cluster	false
tool_settings	wg_dotplot	run_on_cluster	false
tool_settings	wg_dotplot	tmp_directory	dotplot
tool_settings	wg_dotplot	use_cache	true
tool_settings	wg_dotplot	wait_for_cluster	false
tool_settings	wg_dotplot_applet	tmp_directory	dotplot_applet
tool_settings	whole_genome_mapping	possible_data_types	go:GO term;interpro:Interpro domain;gene_type:Gene type;duplication_type:Duplication type;mapman:MapMan term
tool_settings	whole_genome_mapping	run_on_cluster	false
tool_settings	whole_genome_mapping	tmp_directory	genome_mapping
tool_settings	whole_genome_mapping	use_cache	true
tool_settings	whole_genome_mapping	wait_for_cluster	false