EBI_MUSCLE

Created: 2008-06-03 06:16:22 Last updated: 2010-12-06 11:04:03

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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.

Note: the WSMuscle service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MUSCLE services (REST or SOAP) should be used instead.

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Workflow Components

Inputs (2)

Name	Description
Email_address	User e-mail address.
Sequences	Sequences to align, fasta format recommended.

Processors (7)

Name	Type	Description
runMuscle	arbitrarywsdl	Submit a MUSCLE analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/muscle#runmuscle_params_content)
Job_params	local	Parameters for MUSCLE.
Contents_list	local	Wrap input data in list
Input_data	local	Add type to input sequences
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/muscle#poll_jobid_type)
Unpack_alignment	local	Convert byte[] from service into srting.
EBI_MUSCLE_poll_job	workflow	Check status of job.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Convert status code into true/false.	job_status	is_done

Outputs (2)

Name	Description
MUSCLE_job_ID	EBI job identifier.
MUSCLE_alignment	Alignment produced by MUSCLE, in fasta format.

Links (10)

Source	Sink
Contents_list:output	runMuscle:content
Email_address	Job_params:email
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runMuscle:params
Sequences	Input_data:content
Get_alignment:output	Unpack_alignment:bytes
runMuscle:jobid	EBI_MUSCLE_poll_job:Job_ID
Unpack_alignment:string	MUSCLE_alignment
runMuscle:jobid	Get_alignment:jobid
runMuscle:jobid	MUSCLE_job_ID

Coordinations (1)

Controller	Target
EBI_MUSCLE_poll_job	Get_alignment

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Hamish McWilliam

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Information Featured In Packs (2)

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EMBL-EBI Web Services (retired)

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Information Statistics

2372 viewings

2350 downloads

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EBI_MUSCLE

Created by Hamish McWilliam on Tuesday 03 June 2008 06:16:22 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 11:04:03 (UTC)

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