EBI WU-BLAST with program and database selection prompts.

Created: 2009-07-04 11:39:54 Last updated: 2010-12-06 10:56:44

Download Workflow

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 meta-data operations: getPrograms and getDatabases.

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/198/download?version=3
[ More Info Expand ]

Workflow Components

Inputs (0)

Processors (9)

Name	Type	Description
Select_database	local	Select the database to search from a selection menu.
Select_program	local	Select the BLAST program to use for the search from a selection menu.
Ask_for_sequence	local	Ask for the input sequence (fasta format recommended) or a sequence Id in "database:id" format (e.g. uniprot:wap_rat).
Ask_for_email	local	Ask for the user's e-mail address.
EBI_WU_BLAST	workflow	Run a BLAST analysis using the EBI's WU-BLAST service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast).
getPrograms	arbitrarywsdl	Get the list of available analysis programs (see http://www.ebi.ac.uk/Tools/webservices/services/wublast#getprograms)
Extract_program_names	local	Extract just the list of names from the meta-data provided by the service.
Extract_database_names	local	Extract just the list of names from the meta-data provided by the service.
getDatabases	arbitrarywsdl	Get the list of available databases (see http://www.ebi.ac.uk/Tools/webservices/services/wublast#getdatabases)

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Done		job_status	is_done

Outputs (3)

Name	Description
BLAST Report	Output report of the BLAST analysis, in the original plain text format,
BLAST_Report_XML	The results of the BLAST search in an XML format provided by the EBI WU-BLAST service.
BLAST_hit_list	List of entry identifiers of the hits found by the BLAST search.

Links (11)

Source	Sink
Ask_for_email:answer	EBI_WU_BLAST:E-mail Address
Ask_for_sequence:answer	EBI_WU_BLAST:Sequence or ID
EBI_WU_BLAST:Hit ID list	BLAST_hit_list
EBI_WU_BLAST:Text Result	BLAST Report
EBI_WU_BLAST:XML Result	BLAST_Report_XML
Extract_database_names:nodelist	Select_database:valueList
Extract_program_names:nodelist	Select_program:valueList
Select_database:answer	EBI_WU_BLAST:Search Database
Select_program:answer	EBI_WU_BLAST:BLAST Program
getDatabases:result	Extract_database_names:xml-text
getPrograms:result	Extract_program_names:xml-text

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Version 3 (latest) (of 3)

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

EBI_WU-BLAST

Information Tags (6)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Private pack

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

4964 viewings

2824 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

EBI WU-BLAST with prompt

Created by Hamish McWilliam on Friday 30 May 2008 22:56:49 (UTC)

Last edited by Hamish McWilliam on Friday 30 May 2008 22:56:50 (UTC)
EBI WU-BLAST with prompt

Created by Hamish McWilliam on Friday 30 May 2008 22:56:49 (UTC)

Last edited by Hamish McWilliam on Monday 02 June 2008 21:30:43 (UTC)

Revision comment:

Add description in workflow.
EBI WU-BLAST with program and database selection prompts.

Created by Hamish McWilliam on Saturday 04 July 2009 11:39:54 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 10:56:44 (UTC)

Revision comment:

Update to obtain values for selection menus from the service's meta-data oprtations. This means that the list of available programs and databases will be insync with those supported by the service.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (5)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

George

EBI Blast (1)

Download

No description

Created: 2007-12-12 | Last updated: 2008-01-15

Taverna 1

Uploader

Hamish McWilliam

EBI_WU-BLAST (1)

Download

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.

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam