Workflow Entry: EBI_InterProScan_tmhmm_signalp

Created at: 01/06/08 @ 11:21:46 Last updated: 26/10/08 @ 20:50:11

Version 4 (latest) (of 4)

Version created on: 26/10/08 @ 20:50:10 by: Hamish McWilliam | Revision comments Expand

Title: EBI_InterProScan_tmhmm_signalp

Type: Taverna 1

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Description

Use the TMHMM and SignalP methods of InterProScan to perform transmembrane and signal peptide prediction. The EBI's InterProScan web service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan) is used.

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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:LPHN2_RAT).

Processors (10)

Name	Type	Description
Unpack_XML_result	local	Unpack byte[] version of result into a string.
Job_params	local	InterProScan job parameters.
Get_XML_result	arbitrarywsdl	Get the XML format result.
Get_text_result	arbitrarywsdl	Get the plain text format result.
runInterProScan	arbitrarywsdl	Submit the InterProScan job.
Input_data	local	Populate input data structure with input sequence and data type.
Content_list	local	Wrap input data in a list.
Unpack_text_result	local	Unpack byte[] version of result into a string.
EBI_InterProScan_poll_job	workflow	Wait for the job to complete.
Format_as_GFF	beanshell

Beanshells (2)

Name	Description	Inputs	Outputs
Is_done	Map status codes into true/false is done flag.	job_status	is_done
Format_as_GFF		interproscan_text_result	gff_result

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.
GFF_result

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
GFF_result	Format_as_GFF:gff_result
Format_as_GFF:interproscan_text_result	Unpack_text_result:string
InterProScan_text_result	Unpack_text_result:string
EBI_InterProScan_poll_job:Job_ID	runInterProScan:jobid
Get_XML_result:jobid	runInterProScan:jobid
Get_text_result:jobid	runInterProScan:jobid
InterProScan_XML_result	Unpack_XML_result:string
Job_ID	runInterProScan:jobid