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EBI_Kalign

Workflow Entry: EBI_Kalign

Created at: 02/06/08 @ 21:28:56 Last updated: 06/12/10 @ 11:39:52

Version 1 (of 1)

Version created on: 02/06/08 @ 21:28:56 by: Hamish McWilliam

Last edited on: 06/12/10 @ 11:39:52 by: Hamish McWilliam

Title: EBI_Kalign

Type: Taverna 1

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Description

Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default.

Note: the WSKalign 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 Kalign services (REST or SOAP) should be used instead.

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Option 1:

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Option 2:

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http://www.myexperiment.org/workflows/217/download?version=1
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Workflow Components

Inputs (3)

Name	Description
Sequences	Sequences to align (fasta format recommended).
Email_address	User e-mail address.
Molecule_type	Molecule type: P for protein or N for nucleotide.

Processors (7)

Name	Type	Description
runKalign	arbitrarywsdl	Submit a Kalign analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#runkalign_params_content) See the Service entry for this web service.
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/kalign#poll_jobid_type) See the Service entry for this web service.
Job_params	local
Contents_list	local
Input_data	local
Unpack_alignment	local
EBI_Kalign_poll_job	workflow

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done

Outputs (2)

Name	Description
Kalign_alignment	The alignment in ClustalW style format.
Kalign_job_id	EBI job identifier.

Links (11)

Source	Sink
Contents_list:output	runKalign:content
Email_address	Job_params:email
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runKalign:params
Sequences	Input_data:content
Get_alignment:output	Unpack_alignment:bytes
Molecule_type	Job_params:moltype
runKalign:jobid	EBI_Kalign_poll_job:Job_ID
Unpack_alignment:string	Kalign_alignment
runKalign:jobid	Get_alignment:jobid
runKalign:jobid	Kalign_job_id

Coordinations (1)

Controller	Target
EBI_Kalign_poll_job	Get_alignment

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

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Hamish McWilliam

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Information Tags (6)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Statistics

581 viewings

926 downloads

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Citations (0)

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Version History

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EBI_Kalign

Created by Hamish McWilliam on Monday 02 June 2008 @ 21:28:56 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 11:39:52 (UTC)