Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSToffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) ise used.
Submit a T-Coffee analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee#runtcoffee_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSTCoffee.wsdl
runTCoffee
T-Coffee parameters
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Wrap input data in list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add type information to input.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Check job status
Check WSTCoffee job status.
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSTCoffee.wsdl
checkStatus
Map job status to true/false
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Fail if job not done.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
EBI job identifier.
Job status
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSTCoffee.wsdl
poll
Convert byte[] from service into string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
User e-mail address.
Sequences to align, fasta format recommended.
EBI job identifer.
T-Coffee alignment in a ClustalW style format.
Completed
EBI_TCoffee_poll_job
Get_alignment
Scheduled
Running