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commands.json
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commands.json
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[
{
"tool": "blastn",
"name": "blastn (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_1_blast.html#blastn",
"supports_special": true,
"params": {
"blastn_query": {
"default_value": "",
"allows_empty": false
},
"blastn_expect": {
"default_value": "0.05",
"allows_empty": false
}
}
},
{
"tool": "tblastn",
"name": "tblastn (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_1_blast.html#tblastn",
"supports_special": true,
"params": {
"tblastn_query": {
"default_value": "",
"allows_empty": false
},
"tblastn_expect": {
"default_value": "0.05",
"allows_empty": false
}
}
},
{
"tool": "tblastx",
"name": "tblastx (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_1_blast.html#tblastx",
"supports_special": true,
"params": {
"tblastx_query": {
"default_value": "",
"allows_empty": false
},
"tblastx_expect": {
"default_value": "0.05",
"allows_empty": false
}
}
},
{
"tool": "add_refs",
"name": "add_refs (P) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#add_refs",
"supports_special": false,
"params": {
"(add_refs_reference": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "add_taxonomy",
"name": "add_taxonomy (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#add-taxonomy",
"supports_special": true,
"params": {
"add_tax_taxonomy_header": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "CGF_and_CGA_CDS_processing",
"name": "CGF_and_CGA_CDS_processing (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#cgf-and-cga-cds-processing",
"supports_special": true,
"params": {
"cgf_cga_start_codon": {
"default_value": "ATG",
"allows_empty": false
},
"cgf_cga_max_size_difference": {
"default_value": "10",
"allows_empty": false
},
"cgf_cga_reference_file": {
"default_value": "",
"allows_empty": false
},
"cgf_cga_pattern": {
"default_value": "\".\"",
"allows_empty": false
},
"cgf_cga_codon_table": {
"default_value": "1",
"allows_empty": false
},
"cgf_cga_isoform_min_word_length": {
"default_value": "",
"allows_empty": false
},
"cgf_cga_isoform_ref_size": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "check_contamination",
"name": "check_contamination (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#check-contamination",
"supports_special": true,
"params": {
"check_cont_taxonomy": {
"default_value": "",
"allows_empty": false
},
"check_cont_category": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "disambiguate",
"name": "disambiguate (M) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#disambiguate",
"supports_special": true,
"params": {}
},
{
"tool": "merge",
"name": "merge (M) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#merge",
"supports_special": false,
"params": {}
},
{
"tool": "prefix",
"name": "prefix (M) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#prefix",
"supports_special": true,
"params": {}
},
{
"tool": "prefix_out",
"name": "prefix_out (M) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#prefix-out",
"supports_special": true,
"params": {}
},
{
"tool": "remove_stops",
"name": "remove_stops (M) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_2_fasta_processing.html#remove-stops",
"supports_special": true,
"params": {}
},
{
"tool": "Clustal_Omega",
"name": "Clustal_Omega (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#clustal-omega",
"supports_special": false,
"params": {}
},
{
"tool": "Clustal_Omega_codons",
"name": "Clustal_Omega_codons (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#clustal-omega-codons",
"supports_special": false,
"params": {}
},
{
"tool": "T-coffee",
"name": "T-coffee (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#t-coffee",
"supports_special": false,
"params": {}
},
{
"tool": "T-coffee_codons",
"name": "T-coffee_codons (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#t-coffee-codons",
"supports_special": false,
"params": {}
},
{
"tool": "get_phylo_taxa",
"name": "get_phylo_taxa (S2) (FASTA-Newick-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#get_phylo_taxa",
"supports_special": false,
"params": {
"get_phylo_taxa_name1": {
"default_value": "",
"allows_empty": false
},
"get_phylo_taxa_name2": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "Fasttree",
"name": "Fasttree (S) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#fasttree",
"supports_special": false,
"params": {}
},
{
"tool": "FastRoot",
"name": "Fastroot (SP) (Newick- Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#Fastroot",
"supports_special": false,
"params": {
"fastroot_rooting_method": {
"default_value": "MP",
"allows_empty": false
},
"fastroot_outgroup": {
"default_value": "",
"allows_empty": false
}
}
},
{
"tool": "Mafft",
"name": "Mafft (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#Mafft",
"supports_special": false,
"params": {}
},
{
"tool": "Mafft_codons",
"name": "Mafft_codons (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#Mafft_codons",
"supports_special": false,
"params": {}
},
{
"tool": "me_tree",
"name": "me_tree (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#me-tree",
"supports_special": false,
"params": {
"me_tree_bootstrap": {
"default_value": "500",
"allows_empty": false
},
"me_tree_treatment": {
"default_value": "\"Complete Deletion\"",
"allows_empty": false
}
}
},
{
"tool": "ml_tree",
"name": "ml_tree (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#ml-tree",
"supports_special": false,
"params": {
"ml_tree_bootstrap": {
"default_value": "500",
"allows_empty": false
},
"ml_tree_treatment": {
"default_value": "\"Complete Deletion\"",
"allows_empty": false
}
}
},
{
"tool": "mp_tree",
"name": "mp_tree (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#mp-tree",
"supports_special": false,
"params": {
"mp_tree_bootstrap": {
"default_value": "500",
"allows_empty": false
},
"mp_tree_treatment": {
"default_value": "\"Complete Deletion\"",
"allows_empty": false
}
}
},
{
"tool": "MrBayes",
"name": "MrBayes (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#mrbayes",
"supports_special": false,
"params": {
"mb_ngen": {
"default_value": "1000000",
"allows_empty": false
},
"mb_burnin": {
"default_value": "2500",
"allows_empty": false
}
}
},
{
"tool": "nj_tree",
"name": "nj_tree (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#nj-tree",
"supports_special": false,
"params": {
"nj_tree_bootstrap": {
"default_value": "500",
"allows_empty": false
},
"nj_tree_treatment": {
"default_value": "\"Complete Deletion\"",
"allows_empty": false
}
}
},
{
"tool": "Probcons",
"name": "Probcons (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#Probcons",
"supports_special": false,
"params": {}
},
{
"tool": "Probcons_codons",
"name": "Probcons_codons (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#Probcons_codons ",
"supports_special": false,
"params": {}
},
{
"tool": "Probcons_refinement",
"name": "Probcons_refinement (S) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_3_alignment.html#Probcons_refinement",
"supports_special": false,
"params": {
"probcons_refin_iterations": {
"default_value": "100",
"allows_empty": false
}
}
},
{
"tool": "Rootdigger",
"name": "Rootdigger (S2) (FASTA-Newick-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#rootdigger",
"supports_special": false,
"params": {
"rootdigger_mode": {
"default_value": "exhaustive",
"allows_empty": false
}
}
},
{
"tool": "tree_collapse",
"name": "tree_collapse (S) (Newick-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#tree-collapse",
"supports_special": false,
"params": {
"tc_taxonomy": {
"default_value": "",
"allows_empty": true
},
"tc_stsm": {
"default_value": "",
"allows_empty": true
}
}
},
{
"tool": "upgma_tree",
"name": "upgma_tree (SP) (FASTA-Newick)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_4_tree_building.html#upgma-tree",
"supports_special": false,
"params": {
"upgma_tree_bootstrap": {
"default_value": "500",
"allows_empty": false
},
"upgma_tree_treatment": {
"default_value": "\"Complete Deletion\"",
"allows_empty": false
}
}
},
{
"tool": "JModel_test",
"name": "JModel_test (S) (FASTA-Text)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_5_model_checking.html#model-checking",
"supports_special": false,
"params": {}
},
{
"tool": "CGA",
"name": "CGA (MP) (FASTA-FASTA)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_6_gene_annotation.html#cga",
"supports_special": false,
"params": {
"cga_expect1": {
"default_value": "0.05",
"allows_empty": false
},
"cga_reference1": {
"default_value": "",
"allows_empty": false
},
"cga_hit_region_window1": {
"default_value": "10000",
"allows_empty": false
},
"cga_expect2": {
"default_value": "0.05",
"allows_empty": false
},
"cga_reference2": {
"default_value": "",
"allows_empty": false
},
"cga_hit_region_window2": {
"default_value": "10000",
"allows_empty": false
},
"cga_min_overlap": {
"default_value": "2000",
"allows_empty": false
},
"cga_reference3": {
"default_value": "",
"allows_empty": false
},
"cga_max_dist": {
"default_value": "18000",
"allows_empty": false
},
"cga_intron_bp": {
"default_value": "500",
"allows_empty": false
},
"cga_min_full_nucleotide_size": {
"default_value": "500",
"allows_empty": false
},
"cga_selection_criterion": {
"default_value": "criterion_3",
"allows_empty": false
},
"cga_selection_correction": {
"default_value": "20",
"allows_empty": false
}
}
},
{
"tool": "ipssa",
"name": "ipssa (MP) (FASTA-Text)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_7_pss_detection.html#ipssa",
"supports_special": false,
"params": {
"ipssa_sequence_limit": {
"default_value": "90",
"allows_empty": false
},
"ipssa_random_seed": {
"default_value": "12345",
"allows_empty": false
},
"ipssa_align_method": {
"default_value": "muscle",
"allows_empty": false
},
"ipssa_tcoffee_min_score": {
"default_value": "3",
"allows_empty": false
},
"ipssa_mrbayes_generations": {
"default_value": "1000000",
"allows_empty": false
},
"ipssa_mrbayes_burnin": {
"default_value": "2500",
"allows_empty": false
},
"ipssa_fubar_sequence_limit": {
"default_value": "90",
"allows_empty": false
},
"ipssa_fubar_runs": {
"default_value": "1",
"allows_empty": false
},
"ipssa_codeml_sequence_limit": {
"default_value": "30",
"allows_empty": false
},
"ipssa_codeml_runs": {
"default_value": "30",
"allows_empty": false
},
"ipssa_codeml_models": {
"default_value": "\"1 2 7 8\"",
"allows_empty": false
},
"ipssa_omegamap_sequence_limit": {
"default_value": "90",
"allows_empty": false
},
"ipssa_omegamap_iterations": {
"default_value": "2500",
"allows_empty": false
},
"ipssa_omegamap_runs": {
"default_value": "2500",
"allows_empty": false
}
}
},
{
"tool": "kaks",
"name": "kaks (SP) (FASTA-Text)",
"url": "http://evolution6.i3s.up.pt/static/auto-phylo/v2/docs/modules_8_divergence_estimates.html#kaks",
"supports_special": false,
"params": {
"kaks_model": {
"default_value": "NG",
"allows_empty": false
},
"kaks_genetic_code ": {
"default_value": "1",
"allows_empty": false
}
}
}
]