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Parameter | Description | Default value | ||
---|---|---|---|---|
Database name (required) | Base name for BLAST DB files. | |||
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 (required) | Path to the BLAST executable. | default | Search type (required) | Selects the type of the BLAST searches. |
Temporary directory | Directory for temporary files. | default | ||
Expected value | Expectation threshold value. | 10 | ||
Annotate as | Name of the result annotations. | misc_feature | ||
Expected value | Expectation threshold value. | 10 | ||
Temporary directory (required) | Directory for temporary files. | defaultblast_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 (-m 7) |
Parameters in Workflow File
Type: blast
Parameter | Parameter in the GUI | Type | ||
---|---|---|---|---|
blast-type | Search type | string Available values are:
| ||
db- | namepath | Database | namepath | string |
db-pathname | Database pathname | string | ||
tool-path | Tool path | string | ||
blasttemp-typedirSearch type | Temporary directory | string Available values are:
| ||
e-val | Expected value | numeric | ||
result-name | Annotate as | string | ||
e-val | Expected value | numeric | ||
temp-dir | Temporary directory | |||
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
The element has 1 input port:
Name in GUI: Input sequence
Name in Workflow File: in-sequence
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sequence | sequence | sequence |
And 1 output port:
Name in GUI: Annotations
Name in Workflow File: out-annotations
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Set of annotations | annotations | annotation-table |