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 1.0 1000 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' 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="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="&gt;run&gt;email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="&gt;run&gt;title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters&gt;alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters&gt;type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters&gt;ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters&gt;window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters&gt;score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters&gt;topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters&gt;pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters&gt;pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters&gt;pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters&gt;pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters&gt;pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters&gt;dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters&gt;gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters&gt;noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters&gt;gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters&gt;gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters&gt;iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters&gt;numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters&gt;output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters&gt;outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;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 false jobId 0 'text/plain' 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="&gt;runResponse&gt;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' false ktup 0 'text/plain' false window 0 'text/plain' false score 0 'text/plain' false topdiags 0 'text/plain' false 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' false 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="&gt;run&gt;parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters&gt;alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters&gt;type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters&gt;ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters&gt;window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters&gt;score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters&gt;topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters&gt;pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters&gt;pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters&gt;pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters&gt;pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters&gt;pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters&gt;dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters&gt;gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters&gt;noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters&gt;gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters&gt;gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters&gt;iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters&gt;numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters&gt;output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters&gt;outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;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 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="&gt;getResult&gt;jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="&gt;getResult&gt;type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname="&gt;getResult&gt;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&gt;name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter&gt;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_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="&gt;getResultResponse&gt;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 '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="&gt;getResult&gt;jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="&gt;getResult&gt;type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname="&gt;getResult&gt;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&gt;name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter&gt;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="&gt;getResultResponse&gt;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="&gt;getResult&gt;jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="&gt;getResult&gt;type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname="&gt;getResult&gt;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&gt;name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter&gt;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="&gt;getResultResponse&gt;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_inputoutputrun_inputemailEmail_addressrun_inputparametersrun_input_2outputrun_outputinputrunparametersrun_input_2sequenceSequencesgetResultparametersgetResult_inputoutputgetResult_inputjobIdrun_outputjobIdgetResult_inputtypeoutvaluegetResult_outputinputgetResultparametersgetResult_guideTreeparametersgetResult_tree_inputoutputgetResult_tree_inputjobIdrun_outputjobIdgetResult_tree_inputtypetreevaluegetResult_tree_outputinputgetResult_guideTreeparametersgetResult_alignmentparametersgetResult_align_inputoutputgetResult_align_inputjobIdrun_outputjobIdgetResult_align_inputtypealnvaluegetResult_align_outputinputgetResult_alignmentparametersstatusJobIdrun_outputjobIdClustalW_alignmentgetResult_align_outputoutputClustalW_guide_treegetResult_tree_outputoutputClustalW_outputgetResult_outputoutputclustalwStatusstatusJob_status 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="&gt;getStatus&gt;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="&gt;getStatusResponse&gt;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_inputoutputgetStatus_inputjobIdJobIdgetStatus_outputinputgetStatusparametersJob_statusgetStatus_outputstatus 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