Blast_Align_and_TreeemailAddress00 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 2013-01-24 15:31:59.317 UTC Sequence00 >sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 2013-01-24 15:19:13.446 UTC Accepts a protein sequence in FASTA format 2013-01-24 15:18:08.465 UTC fastaSeqsClustalW_alignmenttreePhylipFilter_IDsgroup0regex0stringlist1filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true group 0 'text/plain' java.lang.String true filteredlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList 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.InvokematchGroupvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 0 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.InvokeMatchPatternvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [A-Z_0-9]{4,}_*. 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.InvokeSplit_IDsregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex 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.Invokeregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n 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.InvokeREST_UniProtid0responseBody00net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivity GET http://www.uniprot.org/uniprot/{id}.fasta application/xml application/xml String false false false false true id java.lang.String 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.InvokeMerge_FastaSeqsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge 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.InvokeEMBL_EBI_ClustalW2_SOAPSequences0Email_address0ClustalW_alignment00 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 09:40:39.486 UTC net.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.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.InvokeEBI_NCBI_BLASTemail0sequence0getResult_2_output_output00 This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hite to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so 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 09:39:09.765 UTC net.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.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.Invokeclustalw_phylogenyemail0alignment0getResult_output_output00net.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.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.InvokeFilter_IDsgroupmatchGroupvalueFilter_IDsregexMatchPatternvalueFilter_IDsstringlistSplit_IDssplitSplit_IDsregexregexvalueSplit_IDsstringEBI_NCBI_BLASTgetResult_2_output_outputREST_UniProtidFilter_IDsfilteredlistMerge_FastaSeqsstringlistREST_UniProtresponseBodyEMBL_EBI_ClustalW2_SOAPSequencesMerge_FastaSeqsconcatenatedEMBL_EBI_ClustalW2_SOAPEmail_addressemailAddressEBI_NCBI_BLASTemailemailAddressEBI_NCBI_BLASTsequenceSequenceclustalw_phylogenyemailemailAddressclustalw_phylogenyalignmentEMBL_EBI_ClustalW2_SOAPClustalW_alignmentfastaSeqsMerge_FastaSeqsconcatenatedClustalW_alignmentEMBL_EBI_ClustalW2_SOAPClustalW_alignmenttreePhylipclustalw_phylogenygetResult_output_output Katy Wolstencroft 2013-01-24 15:04:08.829 UTC 4c96c0ab-0e91-412f-9e37-14ed91396bfc 2013-01-15 14:18:28.595 UTC 59d4a3ad-2700-43e7-ba08-e4ea5946509f 2013-01-24 15:57:17.336 UTC 0fe656ec-bdc8-4ff8-a142-94eb0dbcafa9 2013-01-15 14:32:38.494 UTC fca232ac-0dcc-4744-baff-6d28279c9904 2013-01-15 14:21:10.248 UTC 7a8fff28-114a-4cfa-856b-ee0eb1533853 2013-01-15 15:22:08.373 UTC 38aa1745-cd20-49cc-84eb-14564b96fbf4 2013-01-15 14:39:25.327 UTC 37a016ec-0df6-4476-bcf4-d43b36763b46 2013-01-15 15:12:58.353 UTC 2243d5cb-9848-48c4-8ee3-b25ae96ce305 2013-01-15 14:22:37.453 UTC 920016f9-5039-4077-b8ed-902cdbf0b59a 2013-01-24 15:15:22.825 UTC 74d8d591-df30-4af3-9f6e-e52d83279c58 2013-01-15 14:17:42.89 UTC 22f650d4-8c43-40cd-89f5-43048e63808c 2013-01-24 15:19:14.291 UTC 3af895d9-4bc4-4654-a996-b8ba8b563115 2013-01-15 14:57:38.328 UTC 56938694-001a-4908-940b-56f7133180ad 2013-01-16 13:29:27.571 UTC f7b952bb-985c-4c3b-ad4c-4c15513ff5fc 2013-01-15 14:52:21.719 UTC 2d7c459f-d27f-4563-84ae-ee08e06eda65 2013-01-25 09:46:11.718 UTC Blast_Align_and_Tree 2013-01-24 15:04:44.899 UTC 938c7747-6982-4542-86f2-db137f781063 2013-01-15 14:23:12.8 UTC a417de5d-1f8d-4e45-b486-6b5d3561f1eb 2013-01-15 15:14:25.239 UTC 13f2cd58-1a1f-4578-83d6-7cff3212dcf1 2013-01-15 14:19:56.378 UTC 52732b79-864a-46f7-8be6-847c2747cc21 2013-01-24 15:28:23.755 UTC 96364917-28d6-4651-94ad-782f4024611e 2013-01-24 15:13:51.204 UTC efb727fa-d8de-47d7-ba27-e93b399be585 2013-01-15 14:54:13.262 UTC 1ec5d517-1406-4218-a640-933b0d11be71 2013-01-25 09:41:59.243 UTC bb46c94b-e0bb-4e86-849f-82108da58b59 2013-01-15 14:45:21.230 UTC d0b36b57-bb94-472c-94b4-5b0c1c50264b 2013-01-15 14:28:04.186 UTC 8d53e60f-f89b-474c-b465-31348cc4ec2c 2013-01-16 13:42:58.536 UTC b7dc1308-d3b4-404e-bdff-43f4e2b7ee6a 2013-01-16 14:21:39.501 UTC 52a66fe3-3a08-41b8-93b2-25206b577fca 2013-01-25 09:39:13.615 UTC 58595067-f4ef-4f4c-976b-8bb8ca82fb39 2013-01-15 14:27:12.798 UTC fb68350b-b23f-4126-84f2-d33a168a3de5 2013-01-15 14:30:45.969 UTC f63e7848-8aca-4678-9645-dcb978eb4f40 2013-01-15 14:18:49.235 UTC 5aea7109-e1ad-45e3-ba0b-e4b91775dbde 2013-01-15 14:43:56.910 UTC e72b7a9c-7f50-4ff1-a309-16f7191b2db4 2013-01-16 13:44:47.511 UTC b94f9a5f-7306-4de7-bf21-7f511bea5526 2013-01-16 14:19:04.797 UTC b4e44f2e-9d6b-45d6-a308-a3d58a00fd33 2013-01-15 14:56:41.994 UTC 3bd310d2-5544-40c7-a441-208c9d939177 2013-01-24 15:17:16.455 UTC 98cb5f99-db85-433e-b08a-5e757ddc9b40 2013-01-15 14:52:37.897 UTC daef49e4-83f6-4337-861b-e1e8eccc40c8 2013-01-15 14:26:33.480 UTC 406738de-9222-4bbb-b1ed-3a4ded4c45fe 2013-01-15 14:53:09.472 UTC d649b204-f41a-4426-996a-4758dc165e66 2013-01-15 14:41:36.993 UTC This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are aligned and returned as results. Finally, the alignment is submitted to the EBI Clustalw_phylogeny service (Nested Workflow: clustalw_phylogeny), and a phylogenetic tree in phylip format is retuned. The workflow returned a list of protein sequences in FASTA format, a Clustalw alignment, and a phylogenetic tree. 2013-01-24 15:17:06.975 UTC 9bf408ee-7b58-415d-a042-922b84708aed 2013-01-15 14:40:46.42 UTC 47117e2b-d3f9-4ab1-9725-5445fed69f35 2013-01-15 15:10:36.771 UTC 98ed5213-a58d-4715-9d4b-bcdc945e2b8a 2013-01-15 14:25:51.62 UTC 5aa2ee45-4247-4f26-949e-97d5779a826e 2013-01-15 14:55:28.829 UTC fe11b391-28ab-4226-b6a1-67c53373daf1 2013-01-15 14:35:43.398 UTC Workflow18JOB_ID00statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>An identifier for the job to check</xsd:documentation></xsd:annotation></s:basetype></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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The status of the job (FINISHED, ERROR, RUNNING, NOT_FOUND or FAILURE)</xsd:documentation></xsd:annotation></s:basetype></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_inputjobIdJOB_IDgetStatus_outputinputgetStatusparametersstatusgetStatus_outputstatus 7dc29b15-f07e-4beb-9c34-2dc56e0355bb 2013-01-16 11:53:30.48 UTC clustal_phylogenyalignment00 CLUSTAL 2.1 multiple sequence alignment sp|P00560|PGK_YEAST MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|G2WA29|G2WA29_YEASK MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7QC39|E7QC39_YEASZ MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7KA32|E7KA32_YEASA MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|C8Z499|C8Z499_YEAS8 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|C7GQM4|C7GQM4_YEAS2 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|B3LU83|B3LU83_YEAS1 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|A6ZTJ3|A6ZTJ3_YEAS7 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7LRY4|E7LRY4_YEASV MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|H0GD00|H0GD00_9SACH MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV ************************************************** sp|P00560|PGK_YEAST LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|G2WA29|G2WA29_YEASK LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7QC39|E7QC39_YEASZ LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7KA32|E7KA32_YEASA LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|C8Z499|C8Z499_YEAS8 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|C7GQM4|C7GQM4_YEAS2 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|B3LU83|B3LU83_YEAS1 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|A6ZTJ3|A6ZTJ3_YEAS7 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7LRY4|E7LRY4_YEASV LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|H0GD00|H0GD00_9SACH LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG ************************************************** sp|P00560|PGK_YEAST PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|G2WA29|G2WA29_YEASK PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7QC39|E7QC39_YEASZ PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7KA32|E7KA32_YEASA PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|C8Z499|C8Z499_YEAS8 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|C7GQM4|C7GQM4_YEAS2 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|B3LU83|B3LU83_YEAS1 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|A6ZTJ3|A6ZTJ3_YEAS7 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7LRY4|E7LRY4_YEASV PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|H0GD00|H0GD00_9SACH PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH ************************************************** sp|P00560|PGK_YEAST ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|G2WA29|G2WA29_YEASK ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7QC39|E7QC39_YEASZ ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7KA32|E7KA32_YEASA ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|C8Z499|C8Z499_YEAS8 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|C7GQM4|C7GQM4_YEAS2 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|B3LU83|B3LU83_YEAS1 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|A6ZTJ3|A6ZTJ3_YEAS7 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7LRY4|E7LRY4_YEASV ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|H0GD00|H0GD00_9SACH ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE ************************************************** sp|P00560|PGK_YEAST NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|G2WA29|G2WA29_YEASK NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7QC39|E7QC39_YEASZ NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7KA32|E7KA32_YEASA NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|C8Z499|C8Z499_YEAS8 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|C7GQM4|C7GQM4_YEAS2 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|B3LU83|B3LU83_YEAS1 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|A6ZTJ3|A6ZTJ3_YEAS7 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7LRY4|E7LRY4_YEASV NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|H0GD00|H0GD00_9SACH NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE ************************************************** sp|P00560|PGK_YEAST IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|G2WA29|G2WA29_YEASK IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7QC39|E7QC39_YEASZ IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7KA32|E7KA32_YEASA IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|C8Z499|C8Z499_YEAS8 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|C7GQM4|C7GQM4_YEAS2 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|B3LU83|B3LU83_YEAS1 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|A6ZTJ3|A6ZTJ3_YEAS7 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7LRY4|E7LRY4_YEASV IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|H0GD00|H0GD00_9SACH IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT ************************************************** sp|P00560|PGK_YEAST DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|G2WA29|G2WA29_YEASK DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7QC39|E7QC39_YEASZ DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7KA32|E7KA32_YEASA DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|C8Z499|C8Z499_YEAS8 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|C7GQM4|C7GQM4_YEAS2 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|B3LU83|B3LU83_YEAS1 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|A6ZTJ3|A6ZTJ3_YEAS7 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7LRY4|E7LRY4_YEASV DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|H0GD00|H0GD00_9SACH DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT ************************************************** sp|P00560|PGK_YEAST KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|G2WA29|G2WA29_YEASK KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7QC39|E7QC39_YEASZ KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7KA32|E7KA32_YEASA KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|C8Z499|C8Z499_YEAS8 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|C7GQM4|C7GQM4_YEAS2 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|B3LU83|B3LU83_YEAS1 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|A6ZTJ3|A6ZTJ3_YEAS7 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7LRY4|E7LRY4_YEASV KALLXEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|H0GD00|H0GD00_9SACH KALLEEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL **** ********************************************* sp|P00560|PGK_YEAST LEGKELPGVAFLSEKK tr|G2WA29|G2WA29_YEASK LEGKELPGVAFLSEKK tr|E7QC39|E7QC39_YEASZ LEGKELPGVAFLSEKK tr|E7KA32|E7KA32_YEASA LEGKELPGVAFLSEKK tr|C8Z499|C8Z499_YEAS8 LEGKELPGVAFLSEKK tr|C7GQM4|C7GQM4_YEAS2 LEGKELPGVAFLSEKK tr|B3LU83|B3LU83_YEAS1 LEGKELPGVAFLSEKK tr|A6ZTJ3|A6ZTJ3_YEAS7 LEGKELPGVAFLSEKK tr|E7LRY4|E7LRY4_YEASV LEGKELPGVAFLSEKK tr|H0GD00|H0GD00_9SACH LEGKELPGVAFLSEKK **************** 2013-01-25 09:44:50.267 UTC accepts a clustalw protein sequence alignment 2013-01-24 15:45:54.8 UTC email00 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 2013-01-24 15:32:05.472 UTC status_reportgetResult_output_outputrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?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_inputparameters0email0output00net.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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>User email address</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="&gt;run&gt;title"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A title to identify the analysis job</xsd:documentation></xsd:annotation></s:basetype><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The list of parameters to be used for launching the analysis</xsd:documentation></xsd:annotation><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="tree" qname="InputParameters&gt;tree"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Tree Format [Determines the outputs that ClustalW produces.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="kimura" qname="InputParameters&gt;kimura"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Distance correction [Controls whether ClustalW attempts to correct for multiple substitutions at the same site. This is recommended to be set 'on' for more divergent sequences and has the effect of stretching branch lengths. For very divergent sequences the distances cannot be reliably corrected.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="tossgaps" qname="InputParameters&gt;tossgaps"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Excludes Gaps [With this option enabled columns where any of the sequences in the input have a gap will be excluded, forcing the alignment to use only positions where information can be included from all sequences.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Clustering Methods [Clustering Methods]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="pim" qname="InputParameters&gt;pim"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Percent Identity Matrix [Output the percentage identity matrix]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Sequence [Phylogeny using an alignment directly entered into the input box in a supported format. Alignment formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is currently a limit of 500 sequences and 1MB of data.]</xsd:documentation></xsd:annotation></s:basetype></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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A unique identifier for the analysis job</xsd:documentation></xsd:annotation></s:basetype></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 tree 0 'text/plain' false kimura 0 'text/plain' false tossgaps 0 'text/plain' false clustering 0 'text/plain' false pim 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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The list of parameters to be used for launching the analysis</xsd:documentation></xsd:annotation><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="tree" qname="InputParameters&gt;tree"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Tree Format [Determines the outputs that ClustalW produces.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="kimura" qname="InputParameters&gt;kimura"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Distance correction [Controls whether ClustalW attempts to correct for multiple substitutions at the same site. This is recommended to be set 'on' for more divergent sequences and has the effect of stretching branch lengths. For very divergent sequences the distances cannot be reliably corrected.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="tossgaps" qname="InputParameters&gt;tossgaps"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Excludes Gaps [With this option enabled columns where any of the sequences in the input have a gap will be excluded, forcing the alignment to use only positions where information can be included from all sequences.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Clustering Methods [Clustering Methods]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="pim" qname="InputParameters&gt;pim"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Percent Identity Matrix [Output the percentage identity matrix]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Sequence [Phylogeny using an alignment directly entered into the input box in a supported format. Alignment formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is currently a limit of 500 sequences and 1MB of data.]</xsd:documentation></xsd:annotation></s:basetype></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.InvokestatusJOB_ID0status00net.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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns=""> <inputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <name>status</name> <depth>0</depth> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> </inputs> <outputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> <name>loop</name> <depth>0</depth> <granularDepth>0</granularDepth> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> </outputs> <classLoaderSharing>workflow</classLoaderSharing> <localDependencies /> <artifactDependencies /> <script>loop = "" + status.equals("RUNNING"); if ("true".matches(loop)) { Thread.sleep(500); }</script> <dependencies /> </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.InvokegetResultparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?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_inputtype0jobId0output00net.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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>An identifier for the job to check</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="&gt;getResult&gt;type"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The renderer to be used to format the output</xsd:documentation></xsd:annotation></s:basetype><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname="&gt;getResult&gt;parameters"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A list of parameters to be passed on to the renderer</xsd:documentation></xsd:annotation><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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The name of the parameter</xsd:documentation></xsd:annotation></s:basetype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter&gt;value"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The parameter value as an array of String</xsd:documentation></xsd:annotation><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.Invoketype_valuevalue00net.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_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"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Base64 encoded data corresponding to the output of the job formatted by the renderer</xsd:documentation></xsd:annotation></s:basetype></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.Invokerunparametersrun_inputoutputrun_inputparametersrun_input_2outputrun_inputemailemailrun_outputinputrunparametersrun_input_2sequencealignmentstatusJOB_IDrun_outputjobIdgetResultparametersgetResult_inputoutputgetResult_inputtypetype_valuevaluegetResult_inputjobIdrun_outputjobIdgetResult_outputinputgetResultparametersstatus_reportstatusstatusgetResult_output_outputgetResult_outputoutput 651ce628-2792-4cb2-a278-8386d69851ba 2013-01-16 13:16:11.852 UTC 443dda04-ff00-466c-9e71-8b133d5cce8a 2013-01-16 13:13:45.705 UTC 0dd91d8e-414f-44e1-8840-fa42650c7ce5 2013-01-16 13:23:52.958 UTC cfc27e98-1cf9-4d95-a4fe-aec9b5043b23 2013-01-25 09:44:53.162 UTC 632445e9-238d-4297-8565-b879c243e564 2013-01-16 12:07:31.943 UTC 1670e09e-294a-4554-85d5-a0c16d578471 2013-01-16 13:41:30.191 UTC This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip. 2013-01-24 15:44:27.698 UTC 7a509422-a069-41fc-ae01-34d90bd6af55 2013-01-16 13:11:09.281 UTC Katy Wolstencroft 2013-01-16 13:42:46.176 UTC 8fc02eb6-3912-4487-87bc-ae31ee552bf1 2013-01-16 13:42:08.616 UTC 16fd2052-4591-4462-a5a9-5fbce75f4fad 2013-01-24 15:46:57.896 UTC clustal_phylogeny 2013-01-16 13:42:34.331 UTC 56c266b5-970f-4895-94a2-b969dff0917d 2013-01-16 13:18:22.999 UTC 5f98399f-4e3a-49c2-90ed-304d619f4b3a 2013-01-24 15:32:07.122 UTC c647509f-a7fa-41ce-a44d-09e76af4056f 2013-01-24 15:31:23.962 UTC 6eb99ce5-bc3d-486b-ad2a-d565becd2dbc 2013-01-24 15:30:18.916 UTC c398cdfd-d999-4929-af67-b1d33974649f 2013-01-16 13:42:46.931 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 94ffd4a8-871f-42f0-a702-5dc9d56779e9 2011-01-11 10:07:49.835 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 EBI_NCBI_BLASTsequence00 >sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1 MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE 2011-01-17 12:45:10.202 UTC Query seqeunce. Either the actual sequence (fasta format recommended) or a database identifer in database:identifier format (e.g. uniprot:wap_rat). 2011-01-17 12:44:43.843 UTC email00 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 2013-01-25 09:37:49.784 UTC getStatus_output_statusgetResult_original_outputgetResult_graphic_output_outputgetResult_2_output_outputrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?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_inputparameters0email0output00net.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="false" unbounded="false" typename="string" name="program" qname="InputParameters&gt;program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters&gt;alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters&gt;scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters&gt;exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters&gt;dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters&gt;match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters&gt;gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters&gt;gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters&gt;filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters&gt;seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters&gt;gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters&gt;align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters&gt;stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters&gt;database"><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: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_2sequence0program0database1stype0scores0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity program 0 'text/plain' false matrix 0 'text/plain' false alignments 0 'text/plain' false scores 0 'text/plain' false exp 0 'text/plain' false dropoff 0 'text/plain' false match_scores 0 'text/plain' false gapopen 0 'text/plain' false gapext 0 'text/plain' false filter 0 'text/plain' false seqrange 0 'text/plain' false gapalign 0 'text/plain' false align 0 'text/plain' false stype 0 'text/plain' false sequence 0 'text/plain' false database 1 l('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="false" unbounded="false" typename="string" name="program" qname="InputParameters&gt;program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters&gt;matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters&gt;alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters&gt;scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters&gt;exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters&gt;dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters&gt;match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters&gt;gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters&gt;gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters&gt;filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters&gt;seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters&gt;gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters&gt;align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters&gt;stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters&gt;database"><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: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.InvokeStatusjobID0getStatus_output_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>1.2</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 = "" + getStatus_output_status.equals("RUNNING"); if ("true".matches(loop)) { Thread.sleep(500); }</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>getStatus_output_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.Invokeprogram_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity blastp 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.Invokedatabase_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity uniprotkb 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.Invokestype_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity protein 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/ncbiblast?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_originalFormatjobId0type0output00net.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.Invokeoutput_outvalue00net.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_graphicparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?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_graphicFormatjobId0type0output00net.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_graphic_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.Invokeoutput_visualvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity visual-png 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_IDlistparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?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_IDListFormatjobId0type0output00net.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_IDList_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.Invokeoutput_idsvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ids 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.Invokescores_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 10 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.Invokerunparametersrun_inputoutputrun_inputparametersrun_input_2outputrun_inputemailemailrun_outputinputrunparametersrun_input_2sequencesequencerun_input_2programprogram_valuevaluerun_input_2databasedatabase_valuevaluerun_input_2stypestype_valuevaluerun_input_2scoresscores_valuevalueStatusjobIDrun_outputjobIdgetResultparametersgetResult_originalFormatoutputgetResult_originalFormatjobIdrun_outputjobIdgetResult_originalFormattypeoutput_outvaluegetResult_outputinputgetResultparametersgetResult_graphicparametersgetResult_graphicFormatoutputgetResult_graphicFormatjobIdrun_outputjobIdgetResult_graphicFormattypeoutput_visualvaluegetResult_graphic_outputinputgetResult_graphicparametersgetResult_IDlistparametersgetResult_IDListFormatoutputgetResult_IDListFormatjobIdrun_outputjobIdgetResult_IDListFormattypeoutput_idsvaluegetResult_IDList_outputinputgetResult_IDlistparametersgetStatus_output_statusStatusgetStatus_output_statusgetResult_original_outputgetResult_outputoutputgetResult_graphic_output_outputgetResult_graphic_outputoutputgetResult_2_output_outputgetResult_IDList_outputoutput f127a274-842a-4856-8335-b7295bcc9bd0 2011-01-11 16:47:31.385 UTC This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hite to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so 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 09:36:59.719 UTC 084a4037-4d35-416b-90f7-2cf0002e6159 2011-01-11 16:57:53.752 UTC 3beea5e2-c4bc-4698-81d3-98cbc5bb323a 2011-01-11 17:04:21.138 UTC e0453c78-ea9c-45f9-8a79-dbc2b88b4f2d 2013-01-15 13:19:32.144 UTC e1acd84e-fd36-4b15-b7ad-df008b8ea126 2013-01-25 09:37:51.314 UTC 4a3dbe1a-27c3-4465-bfb8-e8c77546b3e5 2013-01-25 09:37:00.919 UTC 8bdda622-7e3f-4390-9ac8-ce604cf33f20 2013-01-15 13:23:04.758 UTC Katy Wolstencroft Hamish McWilliam 2011-01-17 12:43:05.219 UTC EBI_NCBI_BLAST 2011-01-17 12:40:14.878 UTC 0e46a027-6d1e-440a-9966-268cdb79a722 2011-01-11 16:51:25.117 UTC 80fa27da-c84d-45cd-b7b4-5f86e195dc47 2011-01-17 12:45:23.671 UTC EMBL_EBI_ClustalW2_SOAPEmail_address00 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 2011-01-17 16:16:18.865 UTC Sequences00 >seq1 MMGSVELNLRETELCLGLPGGD >seq2 MMGSVELNLRETEICLGLPEGD >seq3 MMGLVELNLRETEICLGLPEGD 2011-01-17 16:16:07.724 UTC 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 ClustalW_alignment The sequence alignment. In Clustal format. 2010-12-06 13:06:41.277 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 ClustalW_output Progress output from ClustalW. Useful when diagnosing problems. 2010-12-06 13:08:08.392 UTC Job_ID Job identifier. 2010-12-06 13:08:18.247 UTC Job_status Job status. 2010-12-06 13:08:27.825 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_outputoutputJob_IDrun_outputjobIdJob_statusstatusJob_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 EMBL-EBI ClustalW2_SOAP 2011-01-17 16:23:03.888 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 10:07:49.585 UTC 4cbe4e6c-13d6-4c87-9aea-34bf5cf92aca 2013-01-25 09:40:45.881 UTC 2f13db4b-d3df-4981-9b0b-d07ebf5c5473 2011-01-17 16:27:19.878 UTC 609f649e-b2d6-4163-95c6-1a48a3341b1a 2011-01-11 10:16:23.550 UTC b1606657-3f23-45a7-8730-88a6c13a2e95 2011-01-11 10:14:51.754 UTC Status_jobID00getStatus_output_statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/ncbiblast?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_outputinputgetStatusparametersgetStatus_output_statusgetStatus_outputstatus 479f5c10-89de-4851-9329-4eca70e743e1 2011-01-11 16:37:35.2 UTC 10b2ab29-e2c4-49ca-8667-2d6185696ac8 2011-01-11 16:35:36.301 UTC Status 2011-01-11 16:37:21.331 UTC