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Fasta_string_to_fasta_list

Workflow Entry: Fasta_string_to_fasta_list

Created at: 06/06/08 @ 21:41:28

Version 1 (of 1)

Version created on: 06/06/08 @ 21:41:28 by: Hamish McWilliam | Revision comments Expand

Title: Fasta_string_to_fasta_list

Type: Taverna 1

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Description

Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

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/228/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
fasta_string	String containing one or more fasta sequences.

Processors (2)

Name	Type	Description
Split_into_sequences	local	Split string using a regular expression, to get the individual sequences.
Add_angle	beanshell	For sequences where the angle bracket (>), denoting the start of the fasta formated sequence, was removed during the split, prepend it.

Beanshells (1)

Name	Description	Inputs	Outputs
Add_angle	For sequences where the angle bracket (>), denoting the start of the fasta formated sequence, was removed during the split, prepend it.	stripped_fasta	full_fasta

Outputs (1)

Name	Description
fasta_list	List of fasta sequences.

Links (3)

Source	Sink
fasta_string	Split_into_sequences:string
Add_angle:full_fasta	fasta_list
Split_into_sequences:split	Add_angle:stripped_fasta

Coordinations (0)

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 (2)

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Information Featured In Packs (1)

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Information Ratings (0)

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Information Attributed By (2)

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Information Favourited By (0)

No one

Information Statistics

926 viewings

870 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Fasta_string_to_fasta_list

Created on: Friday 06 June 2008 @ 21:41:28 (GMT)

Created by: Hamish McWilliam

Revision comments:

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This Workflow only has one version.

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Comments (2)

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Surajwa...

Hi Hamish,

I am new to Taverna. I am seeing that all the workflows in Taverna are coded in xsculf language. Is it the only way in which the workflow is coded in Taverna? Where can I find the description about using xsculf? Also how to construct the workflow visually. I am concentrating on creating automatic workflows, so I am trying to find very easy workflow that can be generated automatically.

thanks,

Suraj Waghulde.

Hamish McWilliam

My understanding is that Taverna uses SCUFL as a way of describing the workflow, thus, in its XML form, it is used as the file format. I see no particular reason why these files couldn't be constucted by other programs. I suggest you go to the Taverna website and check out the documentation there for further details of how it works. As for visual construction of Taverna workflows, the Taverna Workbench is the only tool I'm aware of.