EMBL_EBI_ClustalW2_SOAPEmail_address00
2011-01-17 16:16:18.865 UTC
Requires a valid email address in order to execute services hosted at the EBI.
The EBI asks for an email address so that they can contact you about:
Problems with the service which affect your jobs.
Scheduled maintenance which affects services you are using.
Deprecation and retirement of a service you are using.
If you use a fake email, the workflow may be cancelled before execution completes
2013-01-24 15:50:10.145 UTC
Sequences00
Set of sequences to align. These can be in any common sequence format, although fasta format is recommended, and should be input as a single value (i.e. not a list).
2010-12-06 13:04:07.102 UTC
>seq1
MMGSVELNLRETELCLGLPGGD
>seq2
MMGSVELNLRETEICLGLPEGD
>seq3
MMGLVELNLRETEICLGLPEGD
2011-01-17 16:16:07.724 UTC
ClustalW_alignment
CLUSTAL 2.1 multiple sequence alignment
tr|G7PIM7|G7PIM7_MACFA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|Q28886|OPSD_MACFA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|F7ETG0|F7ETG0_MACMU MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|P08100|OPSD_HUMAN MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|H2QNC5|H2QNC5_PANTR MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|H2P9D0|H2P9D0_PONAB MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|G3R589|G3R589_GORGO MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|G1QZM3|G1QZM3_NOMLE MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|F7IEU9|F7IEU9_CALJA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|Q95KU1|OPSD_FELCA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
*************** **********************************
tr|G7PIM7|G7PIM7_MACFA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|Q28886|OPSD_MACFA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
tr|F7ETG0|F7ETG0_MACMU GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|P08100|OPSD_HUMAN GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|H2QNC5|H2QNC5_PANTR GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|H2P9D0|H2P9D0_PONAB GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|G3R589|G3R589_GORGO GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|G1QZM3|G1QZM3_NOMLE GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|F7IEU9|F7IEU9_CALJA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|Q95KU1|OPSD_FELCA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
*************************************:****:*******
2013-01-30 12:41:19.694 UTC
Produces a sequence alignment in Clustal format.
2013-01-30 12:41:11.704 UTC
ClustalW_guide_tree
Guide tree generated during the alignment. Please note this is not a phylogentic tree and does not reflect the final alignment obtained.
2010-12-06 13:07:34.840 UTC
(
seq1:0.09091,
seq2:0.00000,
seq3:0.04545);
2013-01-30 12:55:57.467 UTC
ClustalW_output
CLUSTAL 2.1 Multiple Sequence Alignments
Sequence format is Pearson
Sequence 1: seq1 22 aa
Sequence 2: seq2 22 aa
Sequence 3: seq3 22 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 90
Sequences (1:3) Aligned. Score: 86
Sequences (2:3) Aligned. Score: 95
Guide tree file created: [clustalw2-S20130130-125430-0701-89753557-pg.dnd]
There are 2 groups
Start of Multiple Alignment
Aligning...
Group 1: Sequences: 2 Score:465
Group 2: Sequences: 3 Score:447
Alignment Score 354
CLUSTAL-Alignment file created [clustalw2-S20130130-125430-0701-89753557-pg.aln]
2013-01-30 12:56:43.532 UTC
Reports the service execution status and metadata from ClustalW. Useful when diagnosing problems.
2013-01-30 12:56:36.747 UTC
clustalwStatus
FINISHED
2013-01-30 12:53:59.637 UTC
Reports the status of the asynchronous service call
2013-01-30 12:53:52.337 UTC
runparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl
run
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_inputemail0parameters0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
email
0
'text/plain'
false
title
0
'text/plain'
false
parameters
0
'text/xml'
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output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname=">run>email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname=">run>title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters>alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters>type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters>ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters>window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters>score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters>topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters>pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters>pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters>pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters>pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters>pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters>dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters>noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters>gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters>iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters>numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters>clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters>output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters>outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_outputinput0jobId00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
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jobId
0
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0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="runResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}runResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">runResponse>jobId" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_input_2sequence0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
alignment
0
'text/plain'
false
type
0
'text/plain'
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ktup
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'text/plain'
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window
0
'text/plain'
false
score
0
'text/plain'
false
topdiags
0
'text/plain'
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pairgap
0
'text/plain'
false
pwmatrix
0
'text/plain'
false
pwdnamatrix
0
'text/plain'
false
pwgapopen
0
'text/plain'
false
pwgapext
0
'text/plain'
false
matrix
0
'text/plain'
false
dnamatrix
0
'text/plain'
false
gapopen
0
'text/plain'
false
noendgaps
0
'text/plain'
false
gapext
0
'text/plain'
false
gapdist
0
'text/plain'
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iteration
0
'text/plain'
false
numiter
0
'text/plain'
false
clustering
0
'text/plain'
false
output
0
'text/plain'
false
outorder
0
'text/plain'
false
sequence
0
'text/plain'
false
output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters>alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters>type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters>ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters>window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters>score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters>topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters>pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters>pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters>pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters>pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters>pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters>dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters>noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters>gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters>iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters>numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters>clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters>output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters>outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResultparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl
getResult
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_inputjobId0type0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
jobId
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'text/plain'
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type
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'text/plain'
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'text/xml'
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'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
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net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_outputinput0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
output
0
'application/octet-stream'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeoutvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
out
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_guideTreeparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl
getResult
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_tree_inputjobId0type0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
jobId
0
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type
0
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'text/xml'
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output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_tree_outputinput0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
output
0
'application/octet-stream'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketreevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
tree
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_alignmentparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl
getResult
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_align_inputjobId0type0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
jobId
0
'text/plain'
false
type
0
'text/plain'
false
parameters
1
'text/xml'
false
output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_align_outputinput0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
output
0
'application/octet-stream'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokealnvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
aln-clustalw
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokestatusJobId0Job_status00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<script>loop = "" + Job_status.equals("RUNNING");
if ("true".matches(loop)) {
Thread.sleep(5000);
}</script>
<dependencies />
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>Job_status</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>0</granularDepth>
<name>loop</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity>
true
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputemailrun_inputparametersrun_outputinputrun_input_2sequencegetResultparametersgetResult_inputjobIdgetResult_inputtypegetResult_outputinputgetResult_guideTreeparametersgetResult_tree_inputjobIdgetResult_tree_inputtypegetResult_tree_outputinputgetResult_alignmentparametersgetResult_align_inputjobIdgetResult_align_inputtypegetResult_align_outputinputstatusJobIdClustalW_alignmentClustalW_guide_treeClustalW_outputclustalwStatus
Hamish McWilliam, updated by Katy Wolstencroft
2013-01-24 15:48:57.797 UTC
24411e27-0652-4739-8d66-0814b5d19afb
2013-01-24 15:50:11.485 UTC
2f13db4b-d3df-4981-9b0b-d07ebf5c5473
2011-01-17 16:27:19.878 UTC
b1606657-3f23-45a7-8730-88a6c13a2e95
2011-01-11 10:14:51.754 UTC
e33ecee3-502e-4211-9142-f06ec2c3cf0a
2013-01-30 12:41:30.344 UTC
5bb9cee6-0826-4c14-a8fd-08fd493520c4
2013-01-30 12:54:27.610 UTC
609f649e-b2d6-4163-95c6-1a48a3341b1a
2011-01-11 10:07:49.585 UTC
0c65483e-b31e-4d62-b1d5-791db73c01c3
2013-01-30 12:56:46.557 UTC
EMBL-EBI ClustalW2_SOAP
2011-01-17 16:23:03.888 UTC
4cbe4e6c-13d6-4c87-9aea-34bf5cf92aca
2013-01-25 09:40:45.881 UTC
Perform a ClustalW2 alignment of protein sequences using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).
This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.
2013-01-25 09:40:31.936 UTC
609f649e-b2d6-4163-95c6-1a48a3341b1a
2011-01-11 10:16:23.550 UTC
Job_status_poll_for_ClustalW2__SOAP_JobId00Job_statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdl
getStatus
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
jobId
0
'text/plain'
false
output
0
'text/xml'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatus" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatus"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getStatus>jobId" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_outputinput0status00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
input
0
'text/xml'
java.lang.String
false
status
0
'text/plain'
0
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatusResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname=">getStatusResponse>status" /></s:elements></s:complextype></s:extensions>
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputJob_status
Get job status for a ClustalW2 (SOAP) job.
2010-12-06 12:58:50.727 UTC
Hamish McWilliam
2010-12-06 12:58:14.513 UTC
Job status poll for ClustalW2 (SOAP)
2010-12-06 12:58:32.770 UTC
94ffd4a8-871f-42f0-a702-5dc9d56779e9
2011-01-11 10:07:49.835 UTC