--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/Mismatch and GapCosts (default: Match_1_Mismatch_3_Existence_5_Extension_2) |
|
|
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, |
|
|
|
> |
|
--blastn-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 250) |
--blastn-num-threads |
|
Integer: >= 1 |
Number of threads (default: 1) |
--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, |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_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]> |
|
--blastp-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 250) |
--blastp-num-threads |
|
Integer: >= 1 |
Number of threads (default: 1) |
--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, |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_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]> |
|
--blastx-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 250) |
--blastx-num-threads |
|
Integer: >= 1 |
Number of threads (default: 1) |
--blastx-query-gencode |
|
Integer: >= 1 |
Query genetic code (default: 1) |
--blastx-word-size |
|
Integer: >= 2 |
Word size (default: 3) |
-d, --destination <ClcUrl> |
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 <ClcUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--program |
|
<[blastp, blastn, tblastn,tblastx, blastx]> |
Program |
--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, |
Protein Matrix And Gap Costs (default: BLOSUM62_Existence_11_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]> |
|
--tblastn-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 250) |
--tblastn-num-threads |
|
Integer: >= 1 |
Number of threads (default: 1) |
--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, |
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]> |
|
--tblastx-max-num-hits |
|
Integer: >= 1 |
Maximum number of hits (default: 250) |
--tblastx-num-threads |
|
Integer: >= 1 |
Number of threads (default: 1) |
--tblastx-query-gencode |
|
Integer: >= 1 |
Query genetic code (default: 1) |
--tblastx-word-size |
|
Integer: >= 2 |
Word size (default: 3) |