EBI_InterProScan for Taverna 2

Created: 2010-01-26 14:45:46 Last updated: 2010-11-24 10:04:09

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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.

The checkStatus processor has looping enabled, it will continue as long as the status is RUNNING - but with a 250 ms sleep. (done as a customized Beanshell script to add the sleep, avoiding overload of the checkStatus service)

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Authors (2)

Titles (3)

Descriptions (1)

Dependencies (0)

Inputs (2)

Name	Description
Email_address	Your email address (for EBI statistics on job submissions)
Sequence_or_ID	Sequence or ID

Processors (17)

Name	Type	Description
Input_data	xmlsplitter
Get_XML_result	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl Wsdl Operation poll
Format_as_GFF	beanshell	Script import java.util.StringTokenizer; interproscan_gff = ""; // Split into lines StringTokenizer tok1 = new StringTokenizer(interproscan_text, "\n"); while(tok1.hasMoreElements()) { feat1 = tok1.nextElement(); // Split into fields StringTokenizer tok2 = new StringTokenizer(feat1, "\t"); fieldCount = 0; attributeStr = ""; while(tok2.hasMoreElements()) { fieldCount++; fieldStr = tok2.nextElement(); if(fieldCount < 2) { // First field is the ID interproscan_gff += fieldStr; } // The tool, feature, start and stop else if(fieldCount == 4 \|\| (fieldCount > 5 && fieldCount < 9)) { interproscan_gff += "\t" + fieldStr; } // Score else if(fieldCount == 9) { if(fieldStr.equals("NA")) { interproscan_gff += "\t."; } else { interproscan_gff += "\t" + fieldStr; } } // Matching InterPro entry else if(fieldCount == 12 && !fieldStr.equals("NULL")) { attributeStr += fieldStr; } // Matching InterPro entry name else if(fieldCount == 13 && !fieldStr.equals("NULL")) { attributeStr += " " + fieldStr; } } interproscan_gff += "\t.\t.\tInterProScan"; if(attributeStr.length() > 0) { interproscan_gff += " ; " + attributeStr; } interproscan_gff += "\n"; }
Job_params	xmlsplitter
Unpack_XML_result	localworker	Script string = new String(bytes);
Get_text_result	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl Wsdl Operation poll
runInterProScan	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl Wsdl Operation runInterProScan
Content_list	xmlsplitter
Unpack_text_result	localworker	Script string = new String(bytes);
Input_data_type_defaultValue	stringconstant	Value sequence
Get_XML_result_type_defaultValue	stringconstant	Value toolxml
Job_params_crc_defaultValue	stringconstant	Value 1
Job_params_seqtype_defaultValue	stringconstant	Value p
Job_params_goterms_defaultValue	stringconstant	Value 1
Job_params_async_defaultValue	stringconstant	Value 1
Get_text_result_type_defaultValue	stringconstant	Value toolraw
checkStatus	wsdl	Wsdl http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl Wsdl Operation checkStatus

Beanshells (1)

Name	Description	Inputs	Outputs
Format_as_GFF		interproscan_text	interproscan_gff

Outputs (5)

Name	Description
InterProScan_text_result
InterProScan_XML_result
Job_ID
InterProScan_GFF
status

Datalinks (23)

Source	Sink
Sequence_or_ID	Input_data:content
Input_data_type_defaultValue:value	Input_data:type
runInterProScan:jobid	Get_XML_result:jobid
Get_XML_result_type_defaultValue:value	Get_XML_result:type
Unpack_text_result:string	Format_as_GFF:interproscan_text
Job_params_seqtype_defaultValue:value	Job_params:seqtype
Job_params_crc_defaultValue:value	Job_params:crc
Job_params_goterms_defaultValue:value	Job_params:goterms
Job_params_async_defaultValue:value	Job_params:async
Email_address	Job_params:email
Get_XML_result:result	Unpack_XML_result:bytes
Get_text_result_type_defaultValue:value	Get_text_result:type
runInterProScan:jobid	Get_text_result:jobid
Content_list:output	runInterProScan:content
Job_params:output	runInterProScan:params
Input_data:output	Content_list:WSArrayofData
Get_text_result:result	Unpack_text_result:bytes
runInterProScan:jobid	checkStatus:jobid
Unpack_text_result:string	InterProScan_text_result
Unpack_XML_result:string	InterProScan_XML_result
runInterProScan:jobid	Job_ID
Format_as_GFF:interproscan_gff	InterProScan_GFF
checkStatus:status	status

Coordinations (2)

Controller	Target
checkStatus	Get_text_result
checkStatus	Get_XML_result

Information Workflow Type

Taverna 2

Information Uploader

Stian Soiland-Reyes

Information License

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Taverna 2.1 beta 2 example workflows

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Information Statistics

7059 viewings

3132 downloads

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Citations (0)

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Version History

In chronological order:

EBI InterproScan (T2, looping)

Created by Stian Soiland-Reyes on Friday 03 July 2009 13:59:27 (UTC)

Last edited by Stian Soiland-Reyes on Friday 03 July 2009 14:00:55 (UTC)
EBI_InterProScan for Taverna 2

Created by Stian Soiland-Reyes on Tuesday 26 January 2010 14:45:46 (UTC)

Last edited by Alan Williams on Wednesday 24 November 2010 10:04:09 (UTC)

Revision comment:

modified looping to include 2.1 support for delays

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EBI InterProScan. Stop fannying around with BLAST and use InterProScan instead.

Created: 2007-10-03

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EBI_InterProScan (3)

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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 ...

Created: 2008-10-26 | Last updated: 2011-04-01

Credits: Hamish McWilliam

EBI_InterProScan for Taverna 2

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