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EBI_InterProScan

Workflow Entry: EBI_InterProScan

Created at: 26/10/08 @ 20:33:34 Last updated: 01/04/11 @ 08:52:28

Version 3 (latest) (of 3)

Version created on: 26/10/08 @ 20:33:34 by: Hamish McWilliam | Revision comments Expand

Last edited on: 01/04/11 @ 08:52:28 by: Hamish McWilliam

Title: EBI_InterProScan

Type: Taverna 1

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Description

Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services.

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the signatures are returned, which are annotated with the corresponding InterPro and GO term assignments for these signature matches.

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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/204/download?version=3
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Workflow Components

Inputs (2)

Name	Description
Email_address	User e-mail address
Sequence_or_ID	Input protein sequence for analysis. This can either be the actual sequence (fasta format recommended) or a database identifier in database:identifer format (e.g. uniprot:wap_rat).

Processors (10)

Name	Type	Description
Input_data	local	Populate input data structure with input sequence and data type.
Unpack_XML_result	local	Unpack byte[] version of result into a string.
Content_list	local	Wrap input data in a list.
Unpack_text_result	local	Unpack byte[] version of result into a string.
Job_params	local	InterProScan job parameters.
Format_as_GFF	beanshell	Using the text output of InterProScan generate GFF format (see http://www.sanger.ac.uk/Software/formats/GFF/) output.
Get_text_result	arbitrarywsdl	Get the plain text format result. See the Service entry for this web service.
runInterProScan	arbitrarywsdl	Submit the InterProScan job. See the Service entry for this web service.
Get_XML_result	arbitrarywsdl	Get the XML format result. See the Service entry for this web service.
EBI_InterProScan_poll_job	workflow	Wait for the job to complete.

Beanshells (2)

Name	Description	Inputs	Outputs
Is_done	Map status codes into true/false is done flag.	job_status	is_done
Format_as_GFF	Using the text output of InterProScan generate GFF format (see http://www.sanger.ac.uk/Software/formats/GFF/) output.	interproscan_text	interproscan_gff

Outputs (4)

Name	Description
InterProScan_text_result	InterProScan result in tab delimited plain text format.
InterProScan_XML_result	InterProScan result in XML format.
Job_ID	EBI job identifier for the InterProScan job.
InterProScan_GFF	InterProScan result in plain text GFF format (see http://www.sanger.ac.uk/Software/formats/GFF/).

Links (15)

Source	Sink
Content_list:output	runInterProScan:content
Email_address	Job_params:email
Get_XML_result:result	Unpack_XML_result:bytes
Get_text_result:result	Unpack_text_result:bytes
Input_data:output	Content_list:WSArrayofData
Job_params:output	runInterProScan:params
Sequence_or_ID	Input_data:content
Unpack_text_result:string	Format_as_GFF:interproscan_text
runInterProScan:jobid	EBI_InterProScan_poll_job:Job_ID
runInterProScan:jobid	Get_XML_result:jobid
Unpack_text_result:string	InterProScan_text_result
runInterProScan:jobid	Get_text_result:jobid
Format_as_GFF:interproscan_gff	InterProScan_GFF
Unpack_XML_result:string	InterProScan_XML_result
runInterProScan:jobid	Job_ID

Coordinations (2)

Controller	Target
EBI_InterProScan_poll_job	Get_text_result
EBI_InterProScan_poll_job	Get_XML_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)

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Information Tags (10)

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Information Featured In Packs (1)

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Information Attributed By (10)

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Information Favourited By (0)

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Information Statistics

5592 viewings

2197 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - EBI_InterProScan

Created on: Saturday 31 May 2008 @ 11:38:57 (GMT)

Created by: Hamish McWilliam

Last edited on: Saturday 31 May 2008 @ 11:38:58 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

None

Previous Versions:
[2] - EBI_InterProScan

Created on: Saturday 31 May 2008 @ 11:38:57 (GMT)

Created by: Hamish McWilliam

Last edited on: Wednesday 25 June 2008 @ 06:30:59 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

Add plain text GFF format output and update some of the meta-data.

Latest Version:
[3] - EBI_InterProScan

Created on: Sunday 26 October 2008 @ 20:33:34 (GMT)

Created by: Hamish McWilliam

Last edited on: Friday 01 April 2011 @ 08:52:28 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

Update for changes to operation output names in web service defintion.

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Comments (1)

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Franck Tanoh	Monday 22 September 2008 @ 16:55:20 (GMT)
	Service " Get_XML_result" doesn't seem to run as a result I was unable to load the workfow in Taverna.