blast

--blastn-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--blastn-lcase-masking <Boolean> Mask lower case (default: false)
--blastn-lcomplex-mask <Boolean> Filter low complexity (default: true)
--blastn-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)
--blastn-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 250)
--blastn-num-threads  
Integer: >= 1 Number of threads (default: 8)
--blastn-word-size  
Integer: >= 2 Word size (default: 11)
--blastp-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--blastp-lcase-masking <Boolean> Mask lower case (default: false)
--blastp-lcomplex-mask <Boolean> Filter low complexity (default: true)
--blastp-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)
--blastp-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 250)
--blastp-num-threads  
Integer: >= 1 Number of threads (default: 8)
--blastp-word-size  
Integer: >= 2 Word size (default: 3)
--blastx-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--blastx-lcase-masking <Boolean> Mask lower case (default: false)
--blastx-lcomplex-mask <Boolean> Filter low complexity (default: true)
--blastx-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)
--blastx-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 250)
--blastx-num-threads  
Integer: >= 1 Number of threads (default: 8)
--blastx-query-gencode  
Integer: >= 1 Query genetic code (default: 1)
--blastx-word-size  
Integer: >= 2 Word size (default: 3)
-d, --destination <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--dbname <String> (default: )
--dbpath <ClcUrl> Blast database path
-i, --input <ClcObjectUrl> Input data on server
--log <Boolean> Enable creation of algo log file. (default: true)
--program <[blastp, blastn, tblastn, tblastx, blastx]> Program (default: blastp)
--subject <ClcUrl> Target
--tblastn-db-gencode  
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--tblastn-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--tblastn-lcase-masking <Boolean> Mask lower case (default: false)
--tblastn-lcomplex-mask <Boolean> Filter low complexity (default: true)
--tblastn-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)
--tblastn-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 250)
--tblastn-num-threads  
Integer: >= 1 Number of threads (default: 8)
--tblastn-word-size  
Integer: >= 2 Word size (default: 3)
--tblastx-db-gencode  
Integer: 1 <= x <= 23 Genetic code to use to translate database/subjects (default: 1)
--tblastx-evalue  
Double: > 0.0 Expectation value (E) threshold for saving hits (default: 10.0)
--tblastx-lcase-masking <Boolean> Mask lower case (default: false)
--tblastx-lcomplex-mask <Boolean> Filter low complexity (default: true)
--tblastx-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)
--tblastx-max-num-hits  
Integer: >= 1 Maximum number of hits (default: 250)
--tblastx-num-threads  
Integer: >= 1 Number of threads (default: 8)
--tblastx-query-gencode  
Integer: >= 1 Query genetic code (default: 1)
--tblastx-word-size  
Integer: >= 2 Word size (default: 3)