Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default.
Run an NCBI BLAST job using the EBI's WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast).
Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default.
Submit a NCBI BLAST analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#runncbiblast_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSNCBIBlast.wsdl
runNCBIBlast
Covert byte[] to string for plain text BLAST output.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type)
toolxml
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSNCBIBlast.wsdl
poll
Covert byte[] to string for XML BLAST output.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the hit identifiers from the analysis result (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#getids_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSNCBIBlast.wsdl
getIds
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSNCBIBlast.wsdl
poll
Parameters for the NCBI BLAST job.
1.0
50
50
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Wrap the input data in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add a type to the input sequence/identifer.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Check if job has completed.
Check the status of a EBI WSNCBIBlast job, and fail if not completed.
Convert job status to true/false.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSNCBIBlast.wsdl
checkStatus
Fail workflow if job not complete.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Identifier for the job to check.
Status of the job checked.
Query seqeunce. Either the actual sequence (fasta format recommended) or a database identifer in database:identifier format (e.g. uniprot:wap_rat).
The database to search (e.g. uniprot).
The BLAST program to use for the search (e.g. blastn, blastp or blastx).
Your e-mail address.
Identifer fot the job at EBI.
The BLAST report output in plain text.
The BLAST report output in XML.
List of identifiers of the hits.
Completed
EBI_NCBI_BLAST_job_poll
getIds
Scheduled
Running
Completed
EBI_NCBI_BLAST_job_poll
Get_text_result
Scheduled
Running
Completed
EBI_NCBI_BLAST_job_poll
Get_XML_result
Scheduled
Running
List of database names for select.
embl,uniprot,pdb
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
List of programs for select.
blastn,blastp,blastx
,
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
Ask for user's e-mail address.
E-mail address
Your e-mail address
net.sourceforge.taverna.scuflworkers.ui.AskWorker
Ask for query sequence, either as sequence or as a database:identifer entry Id.
Sequence or ID
Query sequence or entry ID
net.sourceforge.taverna.scuflworkers.ui.AskWorker
Select the database to search.
Search database
Database
net.sourceforge.taverna.scuflworkers.ui.SelectWorker
Select the program to perform the search.
Program
BLAST program
net.sourceforge.taverna.scuflworkers.ui.SelectWorker