A workflow version of the EMBOSS tutorial

Created: 2011-07-12 15:55:06 Last updated: 2011-07-12 15:55:08

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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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http://www.myexperiment.org/workflows/2226/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (15)

Name	Type	Description
sequenceid	stringconstant	Value swallid:ops2_*
msfFormat	stringconstant	Value msf
send	stringconstant	Value 1171
sbegin	stringconstant	Value 110
transeqSequenceID	stringconstant	Value embl:xlrhodop
prophecyName	stringconstant	Value Ops2 Sequences
prophecyType	stringconstant	Value G
seqret	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret
formatSequences	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret
emma	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma
prettyplot	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/display.prettyplot
tmap	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/protein_2d_structure.tmap
transeq	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq
prophecy	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophecy
prophet	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophet

Beanshells (0)

Outputs (3)

Name	Description
outputPlot
tmapPlot
prophetOutput

Datalinks (17)

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