Workflow Entry: EBI_CENSOR

Created at: 17/06/08 @ 20:42:47 Last updated: 25/06/08 @ 06:16:03

Version 2 (latest) (of 2)

Version created on: 17/06/08 @ 20:42:46 by: Hamish McWilliam | Revision comments Expand

Last edited on: 25/06/08 @ 06:16:03 by: Hamish McWilliam

Title: EBI_CENSOR

Type: Taverna 1

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Description

The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI’s WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.

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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/244/download?version=2
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Workflow Components

Inputs (3)

Name	Description
Email	User e-mail address.
Sequence_or_ID	Input sequence. Either an actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. embl:AJ608703).
Repeat_library	Library of complex repeats to search against (e.g. Fungi).

Processors (11)

Name	Type	Description
Unpack_alignment	local	Unpack the byte[] from the service into a string.
Contents_list	local	Wrap the input data in a list.
Job_params	local	Parameters structure for the job.
Input_data	local	Add type information to the input data.
Unpack_masked_sequence	local	Unpack the byte[] from the service into a string.
Unpack_table	local	Unpack the byte[] from the service into a string.
Get_table	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
runCensor	arbitrarywsdl	Submit a CENSOR analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#runcensor_params_content)
EBI_CENSOR_poll_job	workflow	Check status of a WSCensor job.
Get_masked_sequence	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)

Outputs (4)

Name	Description
CENSOR_job_ID	EBI job identifer for the job.
CENSOR_masked_sequence	Repeat masked sequence in fasta format.
CENSOR_alignment	Alignments of the repeat signature sequences with the masked regions.
CENSOR_table	Table describing masked regions and identified repeats.

Links (17)

Sink	Source
runCensor:content	Contents_list:output
Job_params:email	Email
Unpack_alignment:bytes	Get_alignment:output
Unpack_masked_sequence:bytes	Get_masked_sequence:output
Unpack_table:bytes	Get_table:output
Contents_list:WSArrayofData	Input_data:output
runCensor:params	Job_params:output
Job_params:lib	Repeat_library
Input_data:content	Sequence_or_ID
CENSOR_alignment	Unpack_alignment:string
CENSOR_table	Unpack_table:string
EBI_CENSOR_poll_job:Job_ID	runCensor:jobid
Get_alignment:jobid	runCensor:jobid
Get_masked_sequence:jobid	runCensor:jobid
Get_table:jobid	runCensor:jobid
CENSOR_masked_sequence	Unpack_masked_sequence:string
CENSOR_job_ID	runCensor:jobid