Workflow Entry: Sequence_or_ID

Created at: 01/06/08 @ 14:15:12

Version 1 (of 1)

Version created on: 01/06/08 @ 14:15:12 by: Hamish McWilliam | Revision comments Expand

Title: Sequence_or_ID

Type: Taverna 1

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Description

Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format.

If a sequence identifier, in database:identifier format, is input the EBI’s WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

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Workflow Components

Inputs (1)

Name	Description
Sequence_or_ID	Either an actual sequence or an entry identifer in database:identifier format (e.g. uniprot:wap_rat).

Processors (5)

Name	Type	Description
Is_sequence	beanshell	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).
Fail_if_identifer	local	Fails if the workflow input is an identifier (i.e. is an actual sequence).
Fail_if_sequence	local	Fails if the workflow input was a sequence (i.e. is an identifer).
fetchData	arbitrarywsdl	Fetch the sequence in fasta format from the identifer using EBI's WSDbfetch service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
seqret	soaplabwsdl	Format sequence into fasta format.

Outputs (1)

Name	Description
Sequence	Sequence in fasta format.

Links (7)

Sink	Source
Is_sequence:sequence	Sequence_or_ID
Fail_if_identifer:test	Is_sequence:is_sequence
Fail_if_sequence:test	Is_sequence:is_sequence
fetchData:query	Sequence_or_ID
seqret:sequence_direct_data	Sequence_or_ID
Sequence	fetchData:fetchDataReturn
Sequence	seqret:outseq