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EBI_WU-BLAST

Workflow Entry: EBI_WU-BLAST

Created at: 30/05/08 @ 22:47:18 Last updated: 06/12/10 @ 10:51:04

Version 1 (of 1)

Version created on: 30/05/08 @ 22:47:18 by: Hamish McWilliam

Last edited on: 06/12/10 @ 10:51:04 by: Hamish McWilliam

Title: EBI_WU-BLAST

Type: Taverna 1

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Description

Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params.

Note: the WSWUBlast 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 WU-BLAST services (REST or SOAP) should be used instead.

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Workflow Components

Inputs (4)

Name	Description
Sequence or ID	Input sequence (fasta format recommended) or sequence identifier in database:id format (e.g. uniprot:wap_rat).
Search Database	The name of the database to search (e.g. uniprot).
E-mail Address	Your e-mail address.
BLAST Program	The BLAST program to use for the search (e.g. blastp).

Processors (10)

Name	Type	Description
runWUBlast	arbitrarywsdl	Submit the WU-BLAST job. See the Service entry for this web service.
Decode_XML_Result	local	Unpack the byte[] into a string for display.
Job_params	local	Parameters for the WU-BLAST job.
Get_XML_Result	arbitrarywsdl	Get the XML result for the job. See the Service entry for this web service.
Get_Text_Result	arbitrarywsdl	Get the plain text result for the job. See the Service entry for this web service.
Content_List	local	List of input data items for the job. In the case of WU-BLAST this is a list containing one input sequence.
Get_Hit_ID_List	arbitrarywsdl	Get the list of hit identifiers from the job. See the Service entry for this web service.
Input_Data	local	Pack the input sequence into the structure required.
Poll_Job	workflow	Check if job has completed.
Decode_Text_Result	local	Unpack plain text result from byte[] into a string for display.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Done		job_status	is_done

Outputs (4)

Name	Description
Hit ID list	List of the identifers of the hits found by the search.
Text Result	Plain text BLAST output.
XML Result	XML version of the BLAST output.
Job_ID	Identifier of the job run.

Links (17)

Source	Sink
BLAST Program	Job_params:program
Content_List:output	runWUBlast:content
E-mail Address	Job_params:email
Get_Text_Result:result	Decode_Text_Result:bytes
Get_XML_Result:result	Decode_XML_Result:bytes
Input_Data:output	Content_List:WSArrayofData
Job_params:output	runWUBlast:params
Search Database	Job_params:database
Sequence or ID	Input_Data:content
runWUBlast:jobid	Get_Hit_ID_List:jobid
runWUBlast:jobid	Get_Text_Result:jobid
runWUBlast:jobid	Get_XML_Result:jobid
runWUBlast:jobid	Poll_Job:Job_ID
Decode_Text_Result:string	Text Result
Decode_XML_Result:string	XML Result
Get_Hit_ID_List:result	Hit ID list
runWUBlast:jobid	Job_ID

Coordinations (3)

Controller	Target
Poll_Job	Get_Text_Result
Poll_Job	Get_XML_Result
Poll_Job	Get_Hit_ID_List

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

Information Attributions (0)

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Information Tags (5)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Attributed By (3)

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Information Statistics

1507 viewings

1254 downloads

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Citations (0)

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Version History

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EBI_WU-BLAST

Created by Hamish McWilliam on Friday 30 May 2008 @ 22:47:18 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 10:51:04 (UTC)

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EBI WU-BLAST with program and database sel... (3)

Created: 04/07/09 @ 11:39:54 | Last updated: 06/12/10 @ 10:56:44

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me...