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: Test/gpipe/9606/allcontig_and_rna)
--externalblastnparameters-entrez-query
<[All_organisms, Viruses, Archaea, Limit by entrez query (default: All organisms)
Bacteria,
Fungi, Metazoa, Arthropoda, Eukaryota, Viridiplantae,
Vertebrata,
Primates, Aeropyrum_pernix, Mammalia, Rodentia,
Arabidopsis_thaliana,
Bacillus_subtilis,
Caenorhabditis_elegans, Bos_taurus,
Canis_familiaris,
Dictyostelium_discoideum, Danio_rerio,
Escherichia_coli, Gallus_gallus,
Human_immunodeficiency_virus_type_1,
Mus_musculus, Oryctolagus_cuniculus,
Oryza_sativa,
Plasmodium_falciparum, Ovis_aries,
Saccharomyces_cerevisiae,
Xenopus_tropicalis,
Sus_scrofa, Synechocystis_PCC6803,
Takifugu_rubripes,
Zea_mays]> Xenopus_laevis,
--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/Mismatch and GapCosts (default: Match_1_Mismatch_3_Existence_5_Extension_2)
Match_1_Mismatch_4_Existence_1_Extension_2,
Match_1_Mismatch_4_Existence_2_Extension_1,
Match_1_Mismatch_3_Existence_5_Extension_2,
Match_1_Mismatch_3_Existence_1_Extension_2,
Match_1_Mismatch_3_Existence_2_Extension_1,
Match_1_Mismatch_2_Existence_5_Extension_2,
Match_1_Mismatch_2_Existence_1_Extension_2,
Match_1_Mismatch_2_Existence_3_Extension_1,
Match_1_Mismatch_2_Existence_1_Extension_1,
Match_2_Mismatch_3_Existence_2_Extension_4,
Match_2_Mismatch_3_Existence_3_Extension_3,
Match_2_Mismatch_3_Existence_5_Extension_2,
Match_2_Mismatch_3_Existence_2_Extension_2,
Match_1_Mismatch_1_Existence_3_Extension_2,
Match_1_Mismatch_1_Existence_1_Extension_2,
Match_1_Mismatch_1_Existence_4_Extension_1,
Match_1_Mismatch_1_Existence_2_Extension_1,
Match_4_Mismatch_5_Existence_6_Extension_5,
Match_4_Mismatch_5_Existence_4_Extension_5,
>
--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, Limit by entrez query (default: All organisms)
Bacteria,
Fungi, Metazoa, Arthropoda, Eukaryota, Viridiplantae,
Vertebrata,
Primates, Aeropyrum_pernix, Mammalia, Rodentia,
Arabidopsis_thaliana,
Bacillus_subtilis,
Caenorhabditis_elegans, Bos_taurus,
Canis_familiaris,
Dictyostelium_discoideum, Danio_rerio,
Escherichia_coli, Gallus_gallus,
Human_immunodeficiency_virus_type_1,
Mus_musculus, Oryctolagus_cuniculus,
Oryza_sativa,
Plasmodium_falciparum, Ovis_aries,
Saccharomyces_cerevisiae,
Xenopus_tropicalis,
Sus_scrofa, Synechocystis_PCC6803,
Takifugu_rubripes,
Zea_mays]> Xenopus_laevis,
--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 < Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
PAM30_Existence_6_Extension_2,
PAM30_Existence_10_Extension_1,
PAM30_Existence_8_Extension_1,
PAM70_Existence_7_Extension_2,
PAM70_Existence_11_Extension_1,
PAM70_Existence_9_Extension_1,
BLOSUM80_Existence_7_Extension_2,
BLOSUM80_Existence_11_Extension_1,
BLOSUM80_Existence_9_Extension_1,
BLOSUM62_Existence_8_Extension_2,
BLOSUM62_Existence_12_Extension_1,
BLOSUM62_Existence_10_Extension_1,
BLOSUM45_Existence_12_Extension_3,
BLOSUM45_Existence_10_Extension_3,
BLOSUM45_Existence_14_Extension_2,
BLOSUM45_Existence_12_Extension_2,
BLOSUM45_Existence_18_Extension_1,
BLOSUM45_Existence_16_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, Limit by entrez query (default: All organisms)
Bacteria,
Fungi, Metazoa, Arthropoda, Eukaryota, Viridiplantae,
Vertebrata,
Primates, Aeropyrum_pernix, Mammalia, Rodentia,
Arabidopsis_thaliana,
Bacillus_subtilis,
Caenorhabditis_elegans, Bos_taurus,
Canis_familiaris,
Dictyostelium_discoideum, Danio_rerio,
Escherichia_coli, Gallus_gallus,
Human_immunodeficiency_virus_type_1,
Mus_musculus, Oryctolagus_cuniculus,
Oryza_sativa,
Plasmodium_falciparum, Ovis_aries,
Saccharomyces_cerevisiae,
Xenopus_tropicalis,
Sus_scrofa, Synechocystis_PCC6803,
Takifugu_rubripes,
Zea_mays]> Xenopus_laevis,
--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 < Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
PAM30_Existence_6_Extension_2,
PAM30_Existence_10_Extension_1,
PAM30_Existence_8_Extension_1,
PAM70_Existence_7_Extension_2,
PAM70_Existence_11_Extension_1,
PAM70_Existence_9_Extension_1,
BLOSUM80_Existence_7_Extension_2,
BLOSUM80_Existence_11_Extension_1,
BLOSUM80_Existence_9_Extension_1,
BLOSUM62_Existence_8_Extension_2,
BLOSUM62_Existence_12_Extension_1,
BLOSUM62_Existence_10_Extension_1,
BLOSUM45_Existence_12_Extension_3,
BLOSUM45_Existence_10_Extension_3,
BLOSUM45_Existence_14_Extension_2,
BLOSUM45_Existence_12_Extension_2,
BLOSUM45_Existence_18_Extension_1,
BLOSUM45_Existence_16_Extension_1]>
--externalblastxparameters-max-num-hits
Integer: >= 1 Maximum number of hits (default: 100)
--externalblastxparameters-query-
gencode Query genetic code (default: 1)
Integer: > = 1
--externalblastxparameters-word-size
Integer: >= 2 Word size (default: 3)
--externaltblastnparameters-db <String> Database (default: Test/gpipe/9606/allcontig_and_rna)
--externaltblastnparameters-db-gencode
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--externaltblastnparameters-entrez-
query <[All_organisms, Viruses, Limit by entrez query (default: All organisms)
Archaea,
Viridiplantae, Fungi, Metazoa, Bacteria, Eukaryota,
Arthropoda,
Rodentia, Primates, Aeropyrum_pernix, Vertebrata, Mammalia,
Arabidopsis_thaliana,
Bacillus_subtilis,
Caenorhabditis_elegans, Bos_taurus,
Canis_familiaris,
Dictyostelium_discoideum, Danio_rerio,
Escherichia_coli, Gallus_gallus,
Human_immunodeficiency_virus_type_1,
Mus_musculus, Oryctolagus_cuniculus,
Oryza_sativa,
Plasmodium_falciparum, Ovis_aries,
Saccharomyces_cerevisiae,
Xenopus_tropicalis,
Sus_scrofa, Synechocystis_PCC6803,
Takifugu_rubripes,
Zea_mays]> Xenopus_laevis,
--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 < Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_Extension_1)
PAM30_Existence_6_Extension_2,
PAM30_Existence_10_Extension_1,
PAM30_Existence_8_Extension_1,
PAM70_Existence_7_Extension_2,
PAM70_Existence_11_Extension_1,
PAM70_Existence_9_Extension_1,
BLOSUM80_Existence_7_Extension_2,
BLOSUM80_Existence_11_Extension_1,
BLOSUM80_Existence_9_Extension_1,
BLOSUM62_Existence_8_Extension_2,
BLOSUM62_Existence_12_Extension_1,
BLOSUM62_Existence_10_Extension_1,
BLOSUM45_Existence_12_Extension_3,
BLOSUM45_Existence_10_Extension_3,
BLOSUM45_Existence_14_Extension_2,
BLOSUM45_Existence_12_Extension_2,
BLOSUM45_Existence_18_Extension_1,
BLOSUM45_Existence_16_Extension_1]>
--externaltblastnparameters-max-num-
hits Maximum number of hits (default: 100)
Integer: > = 1
--externaltblastnparameters-word-size
Integer: >= 2 Word size (default: 3)
--externaltblastxparameters-db <String> Database (default: Test/gpipe/9606/allcontig_and_rna)
--externaltblastxparameters-db-gencode
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--externaltblastxparameters-entrez-
query <[All_organisms, Viruses, Limit by entrez query (default: All organisms)
Archaea,
Viridiplantae, Fungi, Metazoa, Bacteria, Eukaryota,
Arthropoda,
Rodentia, Primates, Aeropyrum_pernix, Vertebrata, Mammalia,
Arabidopsis_thaliana,
Bacillus_subtilis,
Caenorhabditis_elegans, Bos_taurus,
Canis_familiaris,
Dictyostelium_discoideum, Danio_rerio,
Escherichia_coli, Gallus_gallus,
Human_immunodeficiency_virus_type_1,
Mus_musculus, Oryctolagus_cuniculus,
Oryza_sativa,
Plasmodium_falciparum, Ovis_aries,
Saccharomyces_cerevisiae,
Xenopus_tropicalis,
Sus_scrofa, Synechocystis_PCC6803,
Takifugu_rubripes,
Zea_mays]> Xenopus_laevis,
--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 Maximum number of hits (default: 100)
Integer: > = 1
--externaltblastxparameters-query-
gencode Query genetic code (default: 1)
Integer: > = 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, Matrix (default: BLOSUM62)
PAM30_Existence_8_Extension_1,
PAM70_Existence_7_Extension_2,
PAM70_Existence_11_Extension_1,
PAM70_Existence_9_Extension_1,
BLOSUM80_Existence_7_Extension_2,
BLOSUM80_Existence_11_Extension_1,
BLOSUM80_Existence_9_Extension_1,
BLOSUM62_Existence_8_Extension_2,
BLOSUM62_Existence_12_Extension_1,
BLOSUM62_Existence_10_Extension_1,
BLOSUM45_Existence_12_Extension_3,
BLOSUM45_Existence_10_Extension_3,
BLOSUM45_Existence_14_Extension_2,
BLOSUM45_Existence_12_Extension_2,
BLOSUM45_Existence_18_Extension_1,
BLOSUM45_Existence_16_Extension_1]>
--program
<[blastp, blastn, tblastn,tblastx, blastx]> Program (default: blastp)