Workflow Entry: EBI_FASTA

Created at: 30/05/08 @ 23:50:46 Last updated: 02/06/08 @ 21:31:18

Version 1 (of 1)

Version created on: 30/05/08 @ 23:50:46 by: Hamish McWilliam | Revision comments Expand

Last edited on: 02/06/08 @ 21:31:18 by: Hamish McWilliam

Title: EBI_FASTA

Type: Taverna 1

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Description

Run a FASTA or SSEARCH sequence similarity search using the EBI’s WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta).

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Download Workflow File/Package (SCUFL)

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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/199/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (4)

Name	Description
Sequence_or_ID	Query sequence (fasta format recommended) or sequence identifer in database:identifer format (e.g. uniprot:wap_rat).
Database	The database to search (e.g. uniprot).
E-mail	Your e-mail address.
FASTA_Program	The FASTA program to run (e.g. fasta3, fastf3, fasts3, fastx3, fasty3, tfastx, tfasty).

Processors (10)

Name	Type	Description
runFasta	arbitrarywsdl	Submit the FASTA/SSEARCH job.
Poll_FASTA_Job	workflow	Check for job completion.
Input_data_list	local	Wrap the input sequence in a list.
Input_data	local	Input data structure, adds a type to the input sequence.
FASTA_job_params	local	Parameters for the FASTA/SSEARCH job.
getIds	arbitrarywsdl	Get the hit identifers.
Get_Text_Result	arbitrarywsdl	Get the FASTA report as text.
Get_XML_Result	arbitrarywsdl	Get the FASTA report as XML.
Unpack_Text_Result	local	Unpack plain text FASTA report from byte[] into string.
Unpack_XML_Result	local	Unpack XML FASTA report from byte[] into string.

Outputs (4)

Name	Description
FASTA_Text_Result	FASTA program output as plain text. Note the exact format of the output depends on the chosen FASTA program.
FASTA_XML_Result	FASTA output in an XML format.
Hit_ID_List	List of the identifiers of the hits found.
Job_ID	The identifier of the job at EBI.

Links (17)

Sink	Source
FASTA_job_params:database	Database
FASTA_job_params:email	E-mail
FASTA_job_params:program	FASTA_Program
Unpack_Text_Result:bytes	Get_Text_Result:output
Unpack_XML_Result:bytes	Get_XML_Result:output
Input_data_list:WSArrayofData	Input_data:output
runFasta:content	Input_data_list:output
Input_data:content	Sequence_or_ID
runFasta:params	FASTA_job_params:output
FASTA_Text_Result	Unpack_Text_Result:string
FASTA_XML_Result	Unpack_XML_Result:string
Get_Text_Result:jobid	runFasta:jobid
Get_XML_Result:jobid	runFasta:jobid
Hit_ID_List	getIds:result
getIds:jobid	runFasta:jobid
Job_ID	runFasta:jobid
Poll_FASTA_Job:Job_ID	runFasta:jobid