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Parameter | Description | Default value | ||
---|---|---|---|---|
Search type | Selects the type of the BLAST searches. | blastn | ||
Database path | Path to the database files. | |||
Database name | Base name for BLAST DB files. | |||
Tool path | Path to the BLAST executable. | default | ||
Temporary directory | Directory for temporary files. | default | ||
Expected value | Expectation threshold value. | 10 | ||
Max hits | Specifies the number of best hits from a region of the query to keep. 0 turns it off. If used, 100 is recommended. | 0 | ||
Annotate as | Name of the result annotations. | blast_result | Gapped alignment||
Perform gapped alignment. | use | Gap costs | Cost to create and extend a gap in an alignment. | 2 2 |
Match scores | Reward and penalty for matching and mismatching bases. | 1 -3 | ||
BLAST output | Location of BLAST output file. | |||
BLAST output type | Type of BLAST output file. | XML (-outfmt 5) |
Parameters in Workflow File
Type: blast-plus
Parameter | Parameter in the GUI | Type | |||
---|---|---|---|---|---|
blast-type | Search type | string Available values are:
| |||
db-path | Database path | string | |||
db-name | Database name | string | |||
tool-path | Tool path | string | |||
temp-dir | Temporary directory | string | |||
e-val | Expected value | numeric | |||
max-hits | Max hits | numeric | |||
result-name | Annotate as | string | gapped-aln | Gapped alignment | boolean|
gap-costs | Gap costs | string | |||
match-scores | Match scores | string | |||
blast-output | BLAST output | string | |||
type-output | BLAST output type | string |
Input/Output Ports
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