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EBI_MPsrch

Workflow Entry: EBI_MPsrch

Created at: 02/06/08 @ 21:49:11 Last updated: 06/12/10 @ 10:38:42

Version 1 (of 1)

Version created on: 02/06/08 @ 21:49:11 by: Hamish McWilliam

Last edited on: 06/12/10 @ 10:38:42 by: Hamish McWilliam

Title: EBI_MPsrch

Type: Taverna 1

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Description

Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch).

Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.

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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:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/218/download?version=1
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Workflow Components

Inputs (4)

Name	Description
Email_address	User e-mail address.
MPsrch_program	The MPsrch program to use for the search: mpsrch_pp or mpsrch_ppa
Sequence_or_ID	Query sequence. Either the actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. uniprot:wap_rat).
Search_database	The database to search (e.g. pdb).

Processors (7)

Name	Type	Description
Job_params	local
Unpack_text_result	local
Input_data	local
Content_list	local
runMPsrch	arbitrarywsdl	Submit a MPsrch analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch#runmpsrch_params_content) See the Service entry for this web service.
Get_text_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch#poll_jobid_type) See the Service entry for this web service.
EBI_MPsrch_poll_job	workflow

Beanshells (1)

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

Outputs (2)

Name	Description
Job_ID
MPsrch_text_result

Links (12)

Source	Sink
Email_address	Job_params:email
Job_params:output	runMPsrch:params
MPsrch_program	Job_params:program
Search_database	Job_params:database
Content_list:output	runMPsrch:content
Input_data:output	Content_list:WSArrayofData
Sequence_or_ID	Input_data:content
Get_text_result:output	Unpack_text_result:bytes
Unpack_text_result:string	MPsrch_text_result
runMPsrch:jobid	EBI_MPsrch_poll_job:Job_ID
runMPsrch:jobid	Get_text_result:jobid
runMPsrch:jobid	Job_ID

Coordinations (1)

Controller	Target
EBI_MPsrch_poll_job	Get_text_result

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)

(Workflows/Files)

None

Information Tags (7)

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Information Shared with Groups (0)

None

Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Ratings (0)

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Information Attributed By (0)

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Information Favourited By (0)

No one

Information Statistics

583 viewings

921 downloads

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Citations (0)

None

Version History

In chronological order:

EBI_MPsrch

Created by Hamish McWilliam on Monday 02 June 2008 @ 21:49:11 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 10:38:42 (UTC)