BioXSD example workflow
Created: 2010-10-12 09:19:17
Last updated: 2010-10-12 09:21:55
An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down :(
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Descriptions (3)
An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) |
An attempt to implement in the BioXSD workflow described in |
An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down. |
Dependencies (0)
Inputs (1)
Name |
Description |
querySequence |
A query protein sequence in BioXSD format
|
Processors (11)
Name |
Type |
Description |
getStatus |
workflow |
|
getResult |
workflow |
|
runBlastp |
workflow |
|
alignmentNumber |
stringconstant |
Value5 |
databaseURI |
stringconstant |
ValueSwiss-Prot |
expectValue |
stringconstant |
Value10 |
gapOpenPenalty |
stringconstant |
Value-1 |
matrix_value |
stringconstant |
ValueBLOSUM62 |
wordsize |
stringconstant |
Value0 |
gapExtensionPenalty |
stringconstant |
Value-1 |
getAccessionIds |
xpath |
Xpath Expression/BlastOutput/ns2:BlastOutput_iterations/ns2:Iteration/ns2:Iteration_hits/ns2:Hit/ns2:Hit_accession |
Outputs (4)
Name |
Description |
GetResult_output_BlastOutput |
|
GetResult_output_DbStatus |
|
getStatus_status |
|
getAccessionIds_nodelist |
|
Datalinks (15)
Source |
Sink |
runBlastp:jobId |
getStatus:jobId |
runBlastp:jobId |
getResult:jobId |
querySequence |
runBlastp:querySequence |
alignmentNumber:value |
runBlastp:alignmentNumber |
databaseURI:value |
runBlastp:databaseURI |
expectValue:value |
runBlastp:expectValue |
gapOpenPenalty:value |
runBlastp:gapOpenPenalty |
matrix_value:value |
runBlastp:matrix |
wordsize:value |
runBlastp:wordsize |
gapExtensionPenalty:value |
runBlastp:gapExtensionPenalty |
getResult:blastOutput |
getAccessionIds:xml_text |
getResult:blastOutput |
GetResult_output_BlastOutput |
getResult:dbStatus |
GetResult_output_DbStatus |
getStatus:status |
getStatus_status |
getAccessionIds:nodelist |
getAccessionIds_nodelist |
Coordinations (1)
Controller |
Target |
getStatus |
getResult |
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