blast_ncbi

-d, --destination <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--externalblastnparameters-db <String> Database (default: GPIPE/9606/current/all_top_level GPIPE/9606/current/rna)
--externalblastnparameters-entrez-query <[All_organisms, Viruses, Archaea, Bacteria, Eukaryota, Viridiplantae, Fungi, Metazoa, Arthropoda, Vertebrata, Mammalia, Rodentia, Primates, Aeropyrum_pernix, Aquifex_aeolicus, Arabidopsis_thaliana, Bacillus_subtilis, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Dictyostelium_discoideum, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Human_immunodeficiency_virus_type_1, Methanococcus_jannaschii, Mus_musculus, Oryctolagus_cuniculus, Oryza_sativa, Ovis_aries, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Schizosaccharomyces_pombe, Xenopus_tropicalis, Simian_immunodeficiency_virus, Sus_scrofa, Synechocystis_PCC6803, Takifugu_rubripes, Xenopus_laevis, Zea_mays]> Limit by entrez query (default: All organisms)
--externalblastnparameters-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--externalblastnparameters-lcase-masking <Boolean> Mask lower case (default: false)
--externalblastnparameters-lcomplex-mask <Boolean> Filter low complexity (default: true)
--externalblastnparameters-mask-for-lookup <Boolean> Mask for lookup (default: false)
--externalblastnparameters-mask-human-repeats <Boolean> Mask human repeats (default: false)
--externalblastnparameters-match-mismatch-gapcosts <[Match_1_Mismatch_4_Existence_5_Extension_2, Match_1_Mismatch_4_Existence_1_Extension_2, Match_1_Mismatch_4_Existence_0_Extension_2, Match_1_Mismatch_4_Existence_2_Extension_1, Match_1_Mismatch_4_Existence_1_Extension_1, Match_1_Mismatch_3_Existence_5_Extension_2, Match_1_Mismatch_3_Existence_2_Extension_2, Match_1_Mismatch_3_Existence_1_Extension_2, Match_1_Mismatch_3_Existence_0_Extension_2, Match_1_Mismatch_3_Existence_2_Extension_1, Match_1_Mismatch_3_Existence_1_Extension_1, Match_1_Mismatch_2_Existence_5_Extension_2, Match_1_Mismatch_2_Existence_2_Extension_2, Match_1_Mismatch_2_Existence_1_Extension_2, Match_1_Mismatch_2_Existence_0_Extension_2, Match_1_Mismatch_2_Existence_3_Extension_1, Match_1_Mismatch_2_Existence_2_Extension_1, Match_1_Mismatch_2_Existence_1_Extension_1, Match_2_Mismatch_3_Existence_5_Extension_2, Match_2_Mismatch_3_Existence_4_Extension_4, Match_2_Mismatch_3_Existence_2_Extension_4, Match_2_Mismatch_3_Existence_0_Extension_4, Match_2_Mismatch_3_Existence_3_Extension_3, Match_2_Mismatch_3_Existence_6_Extension_2, Match_2_Mismatch_3_Existence_4_Extension_2, Match_2_Mismatch_3_Existence_2_Extension_2, Match_1_Mismatch_1_Existence_5_Extension_2, Match_1_Mismatch_1_Existence_3_Extension_2, Match_1_Mismatch_1_Existence_2_Extension_2, Match_1_Mismatch_1_Existence_1_Extension_2, Match_1_Mismatch_1_Existence_0_Extension_2, Match_1_Mismatch_1_Existence_4_Extension_1, Match_1_Mismatch_1_Existence_3_Extension_1, Match_1_Mismatch_1_Existence_2_Extension_1, Match_4_Mismatch_5_Existence_12_Extension_8, Match_4_Mismatch_5_Existence_6_Extension_5, Match_4_Mismatch_5_Existence_5_Extension_5, Match_4_Mismatch_5_Existence_4_Extension_5, Match_4_Mismatch_5_Existence_3_Extension_5]> Match/Mismatch and Gap Costs (default: Match_2_Mismatch_3_Existence_5_Extension_2)
--externalblastnparameters-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 100)
--externalblastnparameters-word-size  
Integer: >= 2 Word size (default: 11)
--externalblastpparameters-db <String> Database (default: nr)
--externalblastpparameters-entrez-query <[All_organisms, Viruses, Archaea, Bacteria, Eukaryota, Viridiplantae, Fungi, Metazoa, Arthropoda, Vertebrata, Mammalia, Rodentia, Primates, Aeropyrum_pernix, Aquifex_aeolicus, Arabidopsis_thaliana, Bacillus_subtilis, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Dictyostelium_discoideum, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Human_immunodeficiency_virus_type_1, Methanococcus_jannaschii, Mus_musculus, Oryctolagus_cuniculus, Oryza_sativa, Ovis_aries, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Schizosaccharomyces_pombe, Xenopus_tropicalis, Simian_immunodeficiency_virus, Sus_scrofa, Synechocystis_PCC6803, Takifugu_rubripes, Xenopus_laevis, Zea_mays]> Limit by entrez query (default: All organisms)
--externalblastpparameters-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--externalblastpparameters-lcase-masking <Boolean> Mask lower case (default: false)
--externalblastpparameters-lcomplex-mask <Boolean> Filter low complexity (default: true)
--externalblastpparameters-mask-for-lookup <Boolean> Mask for lookup (default: false)
--externalblastpparameters-mask-human-repeats <Boolean> Mask human repeats (default: false)
--externalblastpparameters-matrix-gapcosts <[PAM30_Existence_7_Extension_2, PAM30_Existence_6_Extension_2, PAM30_Existence_5_Extension_2, PAM30_Existence_10_Extension_1, PAM30_Existence_9_Extension_1, PAM30_Existence_8_Extension_1, PAM70_Existence_8_Extension_2, PAM70_Existence_7_Extension_2, PAM70_Existence_6_Extension_2, PAM70_Existence_11_Extension_1, PAM70_Existence_10_Extension_1, PAM70_Existence_9_Extension_1, BLOSUM80_Existence_8_Extension_2, BLOSUM80_Existence_7_Extension_2, BLOSUM80_Existence_6_Extension_2, BLOSUM80_Existence_11_Extension_1, BLOSUM80_Existence_10_Extension_1, BLOSUM80_Existence_9_Extension_1, BLOSUM62_Existence_9_Extension_2, BLOSUM62_Existence_8_Extension_2, BLOSUM62_Existence_7_Extension_2, BLOSUM62_Existence_12_Extension_1, BLOSUM62_Existence_11_Extension_1, BLOSUM62_Existence_10_Extension_1, BLOSUM45_Existence_13_Extension_3, BLOSUM45_Existence_12_Extension_3, BLOSUM45_Existence_11_Extension_3, BLOSUM45_Existence_10_Extension_3, BLOSUM45_Existence_15_Extension_2, BLOSUM45_Existence_14_Extension_2, BLOSUM45_Existence_13_Extension_2, BLOSUM45_Existence_12_Extension_2, BLOSUM45_Existence_19_Extension_1, BLOSUM45_Existence_18_Extension_1, BLOSUM45_Existence_17_Extension_1, BLOSUM45_Existence_16_Extension_1]> Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
--externalblastpparameters-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 100)
--externalblastpparameters-word-size  
Integer: >= 2 Word size (default: 3)
--externalblastxparameters-db <String> Database (default: nr)
--externalblastxparameters-entrez-query <[All_organisms, Viruses, Archaea, Bacteria, Eukaryota, Viridiplantae, Fungi, Metazoa, Arthropoda, Vertebrata, Mammalia, Rodentia, Primates, Aeropyrum_pernix, Aquifex_aeolicus, Arabidopsis_thaliana, Bacillus_subtilis, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Dictyostelium_discoideum, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Human_immunodeficiency_virus_type_1, Methanococcus_jannaschii, Mus_musculus, Oryctolagus_cuniculus, Oryza_sativa, Ovis_aries, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Schizosaccharomyces_pombe, Xenopus_tropicalis, Simian_immunodeficiency_virus, Sus_scrofa, Synechocystis_PCC6803, Takifugu_rubripes, Xenopus_laevis, Zea_mays]> Limit by entrez query (default: All organisms)
--externalblastxparameters-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--externalblastxparameters-lcase-masking <Boolean> Mask lower case (default: false)
--externalblastxparameters-lcomplex-mask <Boolean> Filter low complexity (default: true)
--externalblastxparameters-mask-for-lookup <Boolean> Mask for lookup (default: false)
--externalblastxparameters-mask-human-repeats <Boolean> Mask human repeats (default: false)
--externalblastxparameters-matrix-gapcosts <[PAM30_Existence_7_Extension_2, PAM30_Existence_6_Extension_2, PAM30_Existence_5_Extension_2, PAM30_Existence_10_Extension_1, PAM30_Existence_9_Extension_1, PAM30_Existence_8_Extension_1, PAM70_Existence_8_Extension_2, PAM70_Existence_7_Extension_2, PAM70_Existence_6_Extension_2, PAM70_Existence_11_Extension_1, PAM70_Existence_10_Extension_1, PAM70_Existence_9_Extension_1, BLOSUM80_Existence_8_Extension_2, BLOSUM80_Existence_7_Extension_2, BLOSUM80_Existence_6_Extension_2, BLOSUM80_Existence_11_Extension_1, BLOSUM80_Existence_10_Extension_1, BLOSUM80_Existence_9_Extension_1, BLOSUM62_Existence_9_Extension_2, BLOSUM62_Existence_8_Extension_2, BLOSUM62_Existence_7_Extension_2, BLOSUM62_Existence_12_Extension_1, BLOSUM62_Existence_11_Extension_1, BLOSUM62_Existence_10_Extension_1, BLOSUM45_Existence_13_Extension_3, BLOSUM45_Existence_12_Extension_3, BLOSUM45_Existence_11_Extension_3, BLOSUM45_Existence_10_Extension_3, BLOSUM45_Existence_15_Extension_2, BLOSUM45_Existence_14_Extension_2, BLOSUM45_Existence_13_Extension_2, BLOSUM45_Existence_12_Extension_2, BLOSUM45_Existence_19_Extension_1, BLOSUM45_Existence_18_Extension_1, BLOSUM45_Existence_17_Extension_1, BLOSUM45_Existence_16_Extension_1]> Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
--externalblastxparameters-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 100)
--externalblastxparameters-query-gencode  
Integer: >= 1 Query genetic code (default: 1)
--externalblastxparameters-word-size  
Integer: >= 2 Word size (default: 3)
--externaltblastnparameters-db <String> Database (default: GPIPE/9606/current/all_top_level GPIPE/9606/current/rna)
--externaltblastnparameters-db-gencode  
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--externaltblastnparameters-entrez-query <[All_organisms, Viruses, Archaea, Bacteria, Eukaryota, Viridiplantae, Fungi, Metazoa, Arthropoda, Vertebrata, Mammalia, Rodentia, Primates, Aeropyrum_pernix, Aquifex_aeolicus, Arabidopsis_thaliana, Bacillus_subtilis, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Dictyostelium_discoideum, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Human_immunodeficiency_virus_type_1, Methanococcus_jannaschii, Mus_musculus, Oryctolagus_cuniculus, Oryza_sativa, Ovis_aries, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Schizosaccharomyces_pombe, Xenopus_tropicalis, Simian_immunodeficiency_virus, Sus_scrofa, Synechocystis_PCC6803, Takifugu_rubripes, Xenopus_laevis, Zea_mays]> Limit by entrez query (default: All organisms)
--externaltblastnparameters-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--externaltblastnparameters-lcase-masking <Boolean> Mask lower case (default: false)
--externaltblastnparameters-lcomplex-mask <Boolean> Filter low complexity (default: true)
--externaltblastnparameters-mask-for-lookup <Boolean> Mask for lookup (default: false)
--externaltblastnparameters-mask-human-repeats <Boolean> Mask human repeats (default: false)
--externaltblastnparameters-matrix-gapcosts <[PAM30_Existence_7_Extension_2, PAM30_Existence_6_Extension_2, PAM30_Existence_5_Extension_2, PAM30_Existence_10_Extension_1, PAM30_Existence_9_Extension_1, PAM30_Existence_8_Extension_1, PAM70_Existence_8_Extension_2, PAM70_Existence_7_Extension_2, PAM70_Existence_6_Extension_2, PAM70_Existence_11_Extension_1, PAM70_Existence_10_Extension_1, PAM70_Existence_9_Extension_1, BLOSUM80_Existence_8_Extension_2, BLOSUM80_Existence_7_Extension_2, BLOSUM80_Existence_6_Extension_2, BLOSUM80_Existence_11_Extension_1, BLOSUM80_Existence_10_Extension_1, BLOSUM80_Existence_9_Extension_1, BLOSUM62_Existence_9_Extension_2, BLOSUM62_Existence_8_Extension_2, BLOSUM62_Existence_7_Extension_2, BLOSUM62_Existence_12_Extension_1, BLOSUM62_Existence_11_Extension_1, BLOSUM62_Existence_10_Extension_1, BLOSUM45_Existence_13_Extension_3, BLOSUM45_Existence_12_Extension_3, BLOSUM45_Existence_11_Extension_3, BLOSUM45_Existence_10_Extension_3, BLOSUM45_Existence_15_Extension_2, BLOSUM45_Existence_14_Extension_2, BLOSUM45_Existence_13_Extension_2, BLOSUM45_Existence_12_Extension_2, BLOSUM45_Existence_19_Extension_1, BLOSUM45_Existence_18_Extension_1, BLOSUM45_Existence_17_Extension_1, BLOSUM45_Existence_16_Extension_1]> Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
--externaltblastnparameters-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 100)
--externaltblastnparameters-word-size  
Integer: >= 2 Word size (default: 3)
--externaltblastxparameters-db <String> Database (default: GPIPE/9606/current/all_top_level GPIPE/9606/current/rna)
--externaltblastxparameters-db-gencode  
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--externaltblastxparameters-entrez-query <[All_organisms, Viruses, Archaea, Bacteria, Eukaryota, Viridiplantae, Fungi, Metazoa, Arthropoda, Vertebrata, Mammalia, Rodentia, Primates, Aeropyrum_pernix, Aquifex_aeolicus, Arabidopsis_thaliana, Bacillus_subtilis, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Dictyostelium_discoideum, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Human_immunodeficiency_virus_type_1, Methanococcus_jannaschii, Mus_musculus, Oryctolagus_cuniculus, Oryza_sativa, Ovis_aries, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Schizosaccharomyces_pombe, Xenopus_tropicalis, Simian_immunodeficiency_virus, Sus_scrofa, Synechocystis_PCC6803, Takifugu_rubripes, Xenopus_laevis, Zea_mays]> Limit by entrez query (default: All organisms)
--externaltblastxparameters-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--externaltblastxparameters-lcase-masking <Boolean> Mask lower case (default: false)
--externaltblastxparameters-lcomplex-mask <Boolean> Filter low complexity (default: true)
--externaltblastxparameters-mask-for-lookup <Boolean> Mask for lookup (default: false)
--externaltblastxparameters-mask-human-repeats <Boolean> Mask human repeats (default: false)
--externaltblastxparameters-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 100)
--externaltblastxparameters-query-gencode  
Integer: >= 1 Query genetic code (default: 1)
--externaltblastxparameters-word-size  
Integer: >= 2 Word size (default: 3)
-i, --input <ClcObjectUrl> Input data on server
--log <Boolean> Enable creation of algo log file. (default: true)
--matrix <[PAM30_Existence_7_Extension_2, PAM30_Existence_6_Extension_2, PAM30_Existence_5_Extension_2, PAM30_Existence_10_Extension_1, PAM30_Existence_9_Extension_1, PAM30_Existence_8_Extension_1, PAM70_Existence_8_Extension_2, PAM70_Existence_7_Extension_2, PAM70_Existence_6_Extension_2, PAM70_Existence_11_Extension_1, PAM70_Existence_10_Extension_1, PAM70_Existence_9_Extension_1, BLOSUM80_Existence_8_Extension_2, BLOSUM80_Existence_7_Extension_2, BLOSUM80_Existence_6_Extension_2, BLOSUM80_Existence_11_Extension_1, BLOSUM80_Existence_10_Extension_1, BLOSUM80_Existence_9_Extension_1, BLOSUM62_Existence_9_Extension_2, BLOSUM62_Existence_8_Extension_2, BLOSUM62_Existence_7_Extension_2, BLOSUM62_Existence_12_Extension_1, BLOSUM62_Existence_11_Extension_1, BLOSUM62_Existence_10_Extension_1, BLOSUM45_Existence_13_Extension_3, BLOSUM45_Existence_12_Extension_3, BLOSUM45_Existence_11_Extension_3, BLOSUM45_Existence_10_Extension_3, BLOSUM45_Existence_15_Extension_2, BLOSUM45_Existence_14_Extension_2, BLOSUM45_Existence_13_Extension_2, BLOSUM45_Existence_12_Extension_2, BLOSUM45_Existence_19_Extension_1, BLOSUM45_Existence_18_Extension_1, BLOSUM45_Existence_17_Extension_1, BLOSUM45_Existence_16_Extension_1]> Matrix (default: BLOSUM62)
--program <[blastp, blastn, tblastn, tblastx, blastx]> Program (default: blastp)