Workflow Entry: A workflow version of the EMBOSS tutorial

Created at: 05/03/08 @ 14:05:20 Last updated: 25/03/08 @ 14:43:35

Version 1 (of 1)

Version created on: 05/03/08 @ 14:05:20 by: Alan Williams | Revision comments Expand

Last edited on: 25/03/08 @ 14:43:35 by: Alan Williams

Title: A workflow version of the EMBOSS tutorial

Type: Taverna 1

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Description

Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

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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/159/download?version=1
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Workflow Components

Inputs (0)

Processors (15)

Name	Type	Description
sequenceid	stringconstant
prophecyType	stringconstant
prophecyName	stringconstant
send	stringconstant
sbegin	stringconstant
msfFormat	stringconstant
transeqSequenceID	stringconstant
prophet	soaplabwsdl	Gapped alignment for profiles
prophecy	soaplabwsdl	Creates matrices/profiles from multiple alignments
tmap	soaplabwsdl	Displays membrane spanning regions
seqret1	soaplabwsdl	Reads and writes (returns) sequences
transeq	soaplabwsdl	Translate nucleic acid sequences
formatSequences	soaplabwsdl	Reads and writes (returns) sequences
emma	soaplabwsdl	Multiple alignment program - interface to ClustalW program
plot	soaplabwsdl	Displays aligned sequences, with colouring and boxing

Beanshells (0)

Outputs (3)

Name	Description
outputPlot	The array of png images returned from the plot processor
prophetOutput
tmapPlot

Links (17)

Source	Sink
sequenceid:value	seqret1:sequence_usa
seqret1:outseq	emma:sequence_direct_data
emma:outseq	plot:sequences_direct_data
plot:Graphics_in_PNG	outputPlot
emma:outseq	prophecy:sequence_direct_data
prophecyType:value	prophecy:type
prophecyName:value	prophecy:name
prophecy:outfile	prophet:infile_direct_data
transeq:outseq	prophet:sequence_direct_data
transeqSequenceID:value	transeq:sequence_usa
sbegin:value	transeq:sbegin
send:value	transeq:send
prophet:outfile	prophetOutput
tmap:Graphics_in_PNG	tmapPlot
seqret1:outseq	formatSequences:sequence_direct_data
formatSequences:outseq	tmap:sequences_direct_data
msfFormat:value	formatSequences:osformat