About | Mailing List | Publications

Log in | Register | Give us Feedback | Invite

Home
»
Workflows
»
EBI_InterProScan

Workflow Entry: EBI_InterProScan

Created at: 31/05/08 @ 11:38:58 Last updated: 26/10/08 @ 20:33:34

Version 3 (latest) (of 3)

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

Title: EBI_InterProScan

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

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.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

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
[ More Info Expand ]

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.
runInterProScan	arbitrarywsdl	Submit the InterProScan job.
Get_XML_result	arbitrarywsdl	Get the XML format result.
EBI_InterProScan_poll_job	workflow	Wait for the job to complete.

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)

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

Coordinations (2)

Controller	Target
EBI_InterProScan_poll_job	Get_text_result
EBI_InterProScan_poll_job	Get_XML_result

Taverna 1 workflow

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under the Creative Commons Attribution 3.0 License.

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (0)

(Workflows/Files)

None

Information Tags (10)

Original Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

EBI Web Services

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (4)

(Workflows/Files)

Information Favourited By (0)

No one

Statistics

465 viewings

362 downloads

Citations (0)

None

Version History

Earliest Version:
[1] - EBI_InterProScan

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

Created by: Hamish McWilliam

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

Last edited by: Hamish McWilliam

Revision comments:

None

Previous Versions:
[2] - EBI_InterProScan

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

Created by: Hamish McWilliam

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

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

Revision comments:

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

Reviews (0)

No reviews yet

Be the first to review!

Comments (1)

View Timeline

Log in to make a comment

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