Workflow Entry: EBI_MAFFT

Created at: 03/06/08 @ 05:55:44

Version 1 (of 1)

Version created on: 03/06/08 @ 05:55:43 by: Hamish McWilliam | Revision comments Expand

Title: EBI_MAFFT

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI’s WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

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/219/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
Email_address	User e-mail address.
Sequences	Sequences to align (fasta format recommended).

Processors (7)

Name	Type	Description
runMafft	arbitrarywsdl	Submit a MAFFT analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#runmafft_params_content)
Job_params	local	MAFFT parameters.
Contents_list	local	Wrap input data in list.
Input_data	local	Add type to input data.
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/mafft#poll_jobid_type)
Unpack_alignment	local	Convert byte[] from service into string.
EBI_MAFFT_poll_job	workflow	Check for job completion.

Outputs (2)

Name	Description
MAFFT_job_ID	EBI job identifier
MAFFT_alignment	MAFFT alignment of sequences. By default in fasta format.

Links (10)

Sink	Source
runMafft:content	Contents_list:output
Job_params:email	Email_address
Contents_list:WSArrayofData	Input_data:output
runMafft:params	Job_params:output
Input_data:content	Sequences
Unpack_alignment:bytes	Get_alignment:result
EBI_MAFFT_poll_job:Job_ID	runMafft:jobid
MAFFT_alignment	Unpack_alignment:string
Get_alignment:jobid	runMafft:jobid
MAFFT_job_ID	runMafft:jobid