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EBI_CENSOR

Workflow Entry: EBI_CENSOR

Created at: 17/06/08 @ 20:42:46 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 comment 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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Option 2:

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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) See the Service entry for this web service.
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type) See the Service entry for this web service.
runCensor	arbitrarywsdl	Submit a CENSOR analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#runcensor_params_content) See the Service entry for this web service.
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) See the Service entry for this web service.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Map the job status code into a true/false value.	job_status	is_done

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)

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

Coordinations (3)

Controller	Target
EBI_CENSOR_poll_job	Get_masked_sequence
EBI_CENSOR_poll_job	Get_alignment
EBI_CENSOR_poll_job	Get_table

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (0)

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None

Information Tags (6)

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Information Shared with Groups (0)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Ratings (1)

Current:

4.0 / 5

(1 rating)

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Information Favourited By (0)

No one

Information Statistics

765 viewings

989 downloads

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Citations (0)

None

Version History

In chronological order:

EBI_CENSOR

Created by Hamish McWilliam on Tuesday 17 June 2008 @ 20:42:46 (UTC)

Last edited by Hamish McWilliam on Tuesday 17 June 2008 @ 20:42:47 (UTC)
EBI_CENSOR

Created by Hamish McWilliam on Tuesday 17 June 2008 @ 20:42:46 (UTC)

Last edited by Hamish McWilliam on Wednesday 25 June 2008 @ 06:16:03 (UTC)

Revision comment:

Complete meta-data for processors and correct a couple of typos.