Perform a ClustalW multiple sequence alignment using the EBI’s WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). The set of sequences to align are the input, the other parameters for the search (see Job_params) are allowed to default.
Submit a ClustalW analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#runclustalw2_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
runClustalW2
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
toolaln
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
tooldnd
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Check for job status, and wait if job not finished.
Check status of job.
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
checkStatus
Map job status into true/false is done flag
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
If job not finished fail.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
EBI job identifier for the job to check.
Status of the job.
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSClustalW2.wsdl
poll
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Sequences to align (fasta format recommended).
User e-mail address.
The alignment in ClustalW format.
Guide tree used to produce the final alignment.
text/xml
EBI job identifier
Completed
EBI_ClustalW2_poll_job
Get_alignment_result
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_guide_tree_result
Scheduled
Running
Completed
EBI_ClustalW2_poll_job
Get_output_result
Scheduled
Running