Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used.
Submit a MUSCLE analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/muscle#runmuscle_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMuscle.wsdl
runMuscle
Parameters for MUSCLE.
fasta
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Wrap input data in list
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add type to input sequences
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/muscle#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMuscle.wsdl
poll
Convert byte[] from service into srting.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Check status of job.
Check MUSCLE job status.
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/muscle#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMuscle.wsdl
checkStatus
Fail if job not complete.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Convert status code into true/false.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
EBI job identifer for MUSCLE job.
Job status
User e-mail address.
Sequences to align, fasta format recommended.
EBI job identifier.
Alignment produced by MUSCLE, in fasta format.
Completed
EBI_MUSCLE_poll_job
Get_alignment
Scheduled
Running