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EBI_MAFFT

Workflow Entry: EBI_MAFFT

Created at: 03/06/08 @ 05:55:43 Last updated: 06/12/10 @ 11:38:58

Version 1 (of 1)

Version created on: 03/06/08 @ 05:55:43 by: Hamish McWilliam

Last edited on: 06/12/10 @ 11:38:58 by: Hamish McWilliam

Title: EBI_MAFFT

Type: Taverna 1

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Description

Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool.

Note: the WSMafft 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 MAFFT services (REST or SOAP) should be used instead.

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

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http://www.myexperiment.org/workflows/219/download?version=1
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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
runMafft	arbitrarywsdl	Submit a MAFFT analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#runmafft_params_content) See the Service entry for this web service.
Job_params	local	MAFFT parameters.
Contents_list	local	Wrap input data in list.
Input_data	local	Add type to input data.
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#poll_jobid_type) See the Service entry for this web service.
Unpack_alignment	local	Convert byte[] from service into string.
EBI_MAFFT_poll_job	workflow	Check for job completion.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Map job status code to true/false.	job_status	is_done

Outputs (2)

Name	Description
MAFFT_job_ID	EBI job identifier
MAFFT_alignment	MAFFT alignment of sequences. By default in fasta format.

Links (10)

Source	Sink
Contents_list:output	runMafft:content
Email_address	Job_params:email
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runMafft:params
Sequences	Input_data:content
Get_alignment:result	Unpack_alignment:bytes
runMafft:jobid	EBI_MAFFT_poll_job:Job_ID
Unpack_alignment:string	MAFFT_alignment
runMafft:jobid	Get_alignment:jobid
runMafft:jobid	MAFFT_job_ID

Coordinations (1)

Controller	Target
EBI_MAFFT_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)

(People/Groups)

Hamish McWilliam

Information Attributions (0)

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Information Tags (6)

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Information Shared with Groups (0)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Favourited By (0)

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Information Statistics

633 viewings

978 downloads

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Citations (0)

None

Version History

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EBI_MAFFT

Created by Hamish McWilliam on Tuesday 03 June 2008 @ 05:55:43 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 11:38:58 (UTC)