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2013-01-24 15:31:59.317 UTCSequence00Accepts a protein sequence in FASTA format2013-01-24 15:18:08.465 UTC>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA2013-01-24 15:19:13.446 UTCfastaSeqs>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|H2QNC5|H2QNC5_PANTR Uncharacterized protein OS=Pan troglodytes GN=ENSG00000163914 PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|H2P9D0|H2P9D0_PONAB Uncharacterized protein OS=Pongo abelii GN=RHO PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|G3R589|G3R589_GORGO Uncharacterized protein OS=Gorilla gorilla gorilla GN=RHO PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|G1QZM3|G1QZM3_NOMLE Uncharacterized protein OS=Nomascus leucogenys GN=RHO PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|G7PIM7|G7PIM7_MACFA Putative uncharacterized protein OS=Macaca fascicularis GN=EGM_03566 PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|F7IEU9|F7IEU9_CALJA Uncharacterized protein OS=Callithrix jacchus GN=LOC100393724 PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFIFGPTGCNAEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIT
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>tr|F7ETG0|F7ETG0_MACMU Uncharacterized protein OS=Macaca mulatta GN=RHO PE=3 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>sp|Q28886|OPSD_MACFA Rhodopsin OS=Macaca fascicularis GN=RHO PE=2 SV=1
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIP
EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEARAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASI
YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
>sp|Q95KU1|OPSD_FELCA Rhodopsin OS=Felis catus GN=RHO PE=1 SV=1
MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSI
YNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA
2013-01-30 11:02:27.835 UTCProduces a list of FASTA format protein sequences in a single file2013-01-30 11:02:03.84 UTCClustalW_alignmentCLUSTAL 2.1 multiple sequence alignment
tr|G7PIM7|G7PIM7_MACFA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|Q28886|OPSD_MACFA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|F7ETG0|F7ETG0_MACMU MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|P08100|OPSD_HUMAN MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|H2QNC5|H2QNC5_PANTR MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|H2P9D0|H2P9D0_PONAB MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|G3R589|G3R589_GORGO MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|G1QZM3|G1QZM3_NOMLE MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
tr|F7IEU9|F7IEU9_CALJA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
sp|Q95KU1|OPSD_FELCA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVL
*************** **********************************
tr|G7PIM7|G7PIM7_MACFA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|Q28886|OPSD_MACFA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
tr|F7ETG0|F7ETG0_MACMU GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|P08100|OPSD_HUMAN GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|H2QNC5|H2QNC5_PANTR GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|H2P9D0|H2P9D0_PONAB GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|G3R589|G3R589_GORGO GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|G1QZM3|G1QZM3_NOMLE GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLH
tr|F7IEU9|F7IEU9_CALJA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
sp|Q95KU1|OPSD_FELCA GFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH
*************************************:****:*******
2013-01-30 11:01:21.209 UTCProduces a protein sequence alignment in ClustalW format.
2013-01-30 12:17:43.955 UTCtreePhylip(
(
(
(
(
(
(
(
tr|G7PIM7|G7PIM7_MACFA:0.00000,
sp|Q28886|OPSD_MACFA:0.00287)
:0.00000,
tr|F7ETG0|F7ETG0_MACMU:0.00000)
:0.00383,
sp|Q95KU1|OPSD_FELCA:0.02203)
:0.00287,
tr|F7IEU9|F7IEU9_CALJA:0.00718)
:0.01006,
sp|P08100|OPSD_HUMAN:0.00000)
:0.00000,
tr|H2QNC5|H2QNC5_PANTR:0.00000)
:0.00000,
tr|H2P9D0|H2P9D0_PONAB:0.00000)
:0.00000,
tr|G3R589|G3R589_GORGO:0.00000,
tr|G1QZM3|G1QZM3_NOMLE:0.00000);2013-01-30 11:03:29.595 UTCProduces a phylogenetic tree in phylip format2013-01-30 11:03:12.865 UTCFilter_IDsgroup0regex0stringlist1filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruegroup0'text/plain'java.lang.Stringtruefilteredlist1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.RegularExpressionStringListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivity0net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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\nnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.RESTActivityGEThttp://www.uniprot.org/uniprot/{id}.fastaapplication/xmlapplication/xmlStringfalsefalsefalsefalsetrueidjava.lang.Stringnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEMBL_EBI_ClustalW2_SOAPSequences0Email_address0ClustalW_alignment00Perform 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 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_NCBI_BLASTemail0sequence0getResult_2_output_output00This 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 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_IDsgroupFilter_IDsregexFilter_IDsstringlistSplit_IDsregexSplit_IDsstringREST_UniProtidMerge_FastaSeqsstringlistEMBL_EBI_ClustalW2_SOAPSequencesEMBL_EBI_ClustalW2_SOAPEmail_addressEBI_NCBI_BLASTemailEBI_NCBI_BLASTsequenceclustalw_phylogenyemailclustalw_phylogenyalignmentfastaSeqsClustalW_alignmenttreePhylip8aae45b3-0ea3-4d79-abc1-fe2079b790d42013-01-30 12:17:55.585 UTCKaty Wolstencroft2013-01-24 15:04:08.829 UTC52732b79-864a-46f7-8be6-847c2747cc212013-01-24 15:28:23.755 UTC9bf408ee-7b58-415d-a042-922b84708aed2013-01-15 14:40:46.42 UTCBlast_Align_and_Tree2013-01-24 15:04:44.899 UTC47117e2b-d3f9-4ab1-9725-5445fed69f352013-01-15 15:10:36.771 UTC3af895d9-4bc4-4654-a996-b8ba8b5631152013-01-15 14:57:38.328 UTC52a66fe3-3a08-41b8-93b2-25206b577fca2013-01-25 09:39:13.615 UTC59d4a3ad-2700-43e7-ba08-e4ea5946509f2013-01-24 15:57:17.336 UTC5aa2ee45-4247-4f26-949e-97d5779a826e2013-01-15 14:55:28.829 UTC920016f9-5039-4077-b8ed-902cdbf0b59a2013-01-24 15:15:22.825 UTC74d8d591-df30-4af3-9f6e-e52d83279c582013-01-15 14:17:42.89 UTCThis 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 UTC938c7747-6982-4542-86f2-db137f7810632013-01-15 14:23:12.8 UTC5aea7109-e1ad-45e3-ba0b-e4b91775dbde2013-01-15 14:43:56.910 UTC13f2cd58-1a1f-4578-83d6-7cff3212dcf12013-01-15 14:19:56.378 UTCd0b36b57-bb94-472c-94b4-5b0c1c50264b2013-01-15 14:28:04.186 UTC2d7c459f-d27f-4563-84ae-ee08e06eda652013-01-25 09:46:11.718 UTCb4e44f2e-9d6b-45d6-a308-a3d58a00fd332013-01-15 14:56:41.994 UTCfca232ac-0dcc-4744-baff-6d28279c99042013-01-15 14:21:10.248 UTC56938694-001a-4908-940b-56f7133180ad2013-01-16 13:29:27.571 UTC22f650d4-8c43-40cd-89f5-43048e63808c2013-01-24 15:19:14.291 UTC96364917-28d6-4651-94ad-782f4024611e2013-01-24 15:13:51.204 UTC3bd310d2-5544-40c7-a441-208c9d9391772013-01-24 15:17:16.455 UTC37a016ec-0df6-4476-bcf4-d43b36763b462013-01-15 15:12:58.353 UTCb94f9a5f-7306-4de7-bf21-7f511bea55262013-01-16 14:19:04.797 UTC58595067-f4ef-4f4c-976b-8bb8ca82fb392013-01-15 14:27:12.798 UTC0fe656ec-bdc8-4ff8-a142-94eb0dbcafa92013-01-15 14:32:38.494 UTC1ec5d517-1406-4218-a640-933b0d11be712013-01-25 09:41:59.243 UTC39cd908b-8e31-42cf-9274-a598c3f090e62013-01-30 11:03:32.270 UTC2243d5cb-9848-48c4-8ee3-b25ae96ce3052013-01-15 14:22:37.453 UTCf7b952bb-985c-4c3b-ad4c-4c15513ff5fc2013-01-15 14:52:21.719 UTC4c96c0ab-0e91-412f-9e37-14ed91396bfc2013-01-15 14:18:28.595 UTC38aa1745-cd20-49cc-84eb-14564b96fbf42013-01-15 14:39:25.327 UTCfe11b391-28ab-4226-b6a1-67c53373daf12013-01-15 14:35:43.398 UTC8d53e60f-f89b-474c-b465-31348cc4ec2c2013-01-16 13:42:58.536 UTC98ed5213-a58d-4715-9d4b-bcdc945e2b8a2013-01-15 14:25:51.62 UTCfb68350b-b23f-4126-84f2-d33a168a3de52013-01-15 14:30:45.969 UTCf63e7848-8aca-4678-9645-dcb978eb4f402013-01-15 14:18:49.235 UTCb7dc1308-d3b4-404e-bdff-43f4e2b7ee6a2013-01-16 14:21:39.501 UTCdaef49e4-83f6-4337-861b-e1e8eccc40c82013-01-15 14:26:33.480 UTCefb727fa-d8de-47d7-ba27-e93b399be5852013-01-15 14:54:13.262 UTC7a8fff28-114a-4cfa-856b-ee0eb15338532013-01-15 15:22:08.373 UTC406738de-9222-4bbb-b1ed-3a4ded4c45fe2013-01-15 14:53:09.472 UTCa417de5d-1f8d-4e45-b486-6b5d3561f1eb2013-01-15 15:14:25.239 UTCd649b204-f41a-4426-996a-4758dc165e662013-01-15 14:41:36.993 UTCe72b7a9c-7f50-4ff1-a309-16f7191b2db42013-01-16 13:44:47.511 UTC98cb5f99-db85-433e-b08a-5e757ddc9b402013-01-15 14:52:37.897 UTCbb46c94b-e0bb-4e86-849f-82108da58b592013-01-15 14:45:21.230 UTCEBI_NCBI_BLASTsequence00>sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1
MAANYSSTSTRREHVKVKTSSQPGFLERLSETSGGMFVGLMAFLLSFYLIFTNEGRALKT
ATSLAEGLSLVVSPDSIHSVAPENEGRLVHIIGALRTSKLLSDPNYGVHLPAVKLRRHVE
MYQWVETEESREYTEDGQVKKETRYSYNTEWRSEIINSKNFDREIGHKNPSAMAVESFMA
TAPFVQIGRFFLSSGLIDKVDNFKSLSLSKLEDPHVDIIRRGDFFYHSENPKYPEVGDLR
VSFSYAGLSGDDPDLGPAHVVTVIARQRGDQLVPFSTKSGDTLLLLHHGDFSAEEVFHRE
LRSNSMKTWGLRAAGWMAMFMGLNLMTRILYTLVDWFPVFRDLVNIGLKAFAFCVATSLT
LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE2011-01-17 12:45:10.202 UTCQuery 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 UTCemail00Requires 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 UTCgetStatus_output_statusgetResult_original_outputgetResult_graphic_output_outputgetResult_2_output_outputrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlrunnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityemail0'text/plain'falsetitle0'text/plain'falseparameters0'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname=">run>email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname=">run>title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters>program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters>alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters>scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters>exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters>dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters>match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters>filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters>seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters>gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters>align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters>stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters>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.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalsejobId0'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=">runResponse>jobId" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityprogram0'text/plain'falsematrix0'text/plain'falsealignments0'text/plain'falsescores0'text/plain'falseexp0'text/plain'falsedropoff0'text/plain'falsematch_scores0'text/plain'falsegapopen0'text/plain'falsegapext0'text/plain'falsefilter0'text/plain'falseseqrange0'text/plain'falsegapalign0'text/plain'falsealign0'text/plain'falsestype0'text/plain'falsesequence0'text/plain'falsedatabase1l('text/plain')falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="program" qname="InputParameters>program" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="int" name="alignments" qname="InputParameters>alignments" /><s:basetype optional="true" unbounded="false" typename="int" name="scores" qname="InputParameters>scores" /><s:basetype optional="true" unbounded="false" typename="string" name="exp" qname="InputParameters>exp" /><s:basetype optional="true" unbounded="false" typename="int" name="dropoff" qname="InputParameters>dropoff" /><s:basetype optional="true" unbounded="false" typename="string" name="match_scores" qname="InputParameters>match_scores" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="int" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="string" name="filter" qname="InputParameters>filter" /><s:basetype optional="true" unbounded="false" typename="string" name="seqrange" qname="InputParameters>seqrange" /><s:basetype optional="true" unbounded="false" typename="boolean" name="gapalign" qname="InputParameters>gapalign" /><s:basetype optional="true" unbounded="false" typename="int" name="align" qname="InputParameters>align" /><s:basetype optional="false" unbounded="false" typename="string" name="stype" qname="InputParameters>stype" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="database" qname="InputParameters>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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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 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xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" 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xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions 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/></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityvisual-pngnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityidsnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivity10net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputparametersrun_inputemailrun_outputinputrun_input_2sequencerun_input_2programrun_input_2databaserun_input_2styperun_input_2scoresStatusjobIDgetResultparametersgetResult_originalFormatjobIdgetResult_originalFormattypegetResult_outputinputgetResult_graphicparametersgetResult_graphicFormatjobIdgetResult_graphicFormattypegetResult_graphic_outputinputgetResult_IDlistparametersgetResult_IDListFormatjobIdgetResult_IDListFormattypegetResult_IDList_outputinputgetStatus_output_statusgetResult_original_outputgetResult_graphic_output_outputgetResult_2_output_output084a4037-4d35-416b-90f7-2cf0002e61592011-01-11 16:57:53.752 UTC3beea5e2-c4bc-4698-81d3-98cbc5bb323a2011-01-11 17:04:21.138 UTCThis 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 UTC0e46a027-6d1e-440a-9966-268cdb79a7222011-01-11 16:51:25.117 UTCKaty Wolstencroft
Hamish McWilliam2011-01-17 12:43:05.219 UTCEBI_NCBI_BLAST2011-01-17 12:40:14.878 UTC8bdda622-7e3f-4390-9ac8-ce604cf33f202013-01-15 13:23:04.758 UTCe1acd84e-fd36-4b15-b7ad-df008b8ea1262013-01-25 09:37:51.314 UTC4a3dbe1a-27c3-4465-bfb8-e8c77546b3e52013-01-25 09:37:00.919 UTC80fa27da-c84d-45cd-b7b4-5f86e195dc472011-01-17 12:45:23.671 UTCf127a274-842a-4856-8335-b7295bcc9bd02011-01-11 16:47:31.385 UTCe0453c78-ea9c-45f9-8a79-dbc2b88b4f2d2013-01-15 13:19:32.144 UTCWorkflow18JOB_ID00statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlgetStatusnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatus" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatus"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getStatus>jobId"><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.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsestatus0'text/plain'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatusResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname=">getStatusResponse>status"><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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputstatus7dc29b15-f07e-4beb-9c34-2dc56e0355bb2013-01-16 11:53:30.48 UTCJob_status_poll_for_ClustalW2__SOAP_JobId00Job_statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdlgetStatusnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatus" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatus"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getStatus>jobId" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsestatus0'text/plain'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatusResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname=">getStatusResponse>status" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputJob_statusJob status poll for ClustalW2 (SOAP)2010-12-06 12:58:32.770 UTCHamish McWilliam2010-12-06 12:58:14.513 UTC94ffd4a8-871f-42f0-a702-5dc9d56779e92011-01-11 10:07:49.835 UTCGet job status for a ClustalW2 (SOAP) job.2010-12-06 12:58:50.727 UTCEMBL_EBI_ClustalW2_SOAPEmail_address002011-01-17 16:16:18.865 UTCRequires 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 completes2013-01-24 15:50:10.145 UTCSequences00>seq1
MMGSVELNLRETELCLGLPGGD
>seq2
MMGSVELNLRETEICLGLPEGD
>seq3
MMGLVELNLRETEICLGLPEGD2011-01-17 16:16:07.724 UTCSet 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 UTCClustalW_alignmentThe sequence alignment. In Clustal format.2010-12-06 13:06:41.277 UTCClustalW_guide_treeGuide 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 UTCClustalW_outputProgress output from ClustalW. Useful when diagnosing problems.2010-12-06 13:08:08.392 UTCJob_IDJob identifier.2010-12-06 13:08:18.247 UTCJob_statusJob status.2010-12-06 13:08:27.825 UTCrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdlrunnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityemail0'text/plain'falsetitle0'text/plain'falseparameters0'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname=">run>email" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname=">run>title" /><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters>alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters>type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters>ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters>window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters>score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters>topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters>pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters>pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters>pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters>pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters>pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters>dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters>noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters>gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters>iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters>numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters>clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters>output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters>outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalsejobId0'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=">runResponse>jobId" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityalignment0'text/plain'falsetype0'text/plain'falsektup0'text/plain'falsewindow0'text/plain'falsescore0'text/plain'falsetopdiags0'text/plain'falsepairgap0'text/plain'falsepwmatrix0'text/plain'falsepwdnamatrix0'text/plain'falsepwgapopen0'text/plain'falsepwgapext0'text/plain'falsematrix0'text/plain'falsednamatrix0'text/plain'falsegapopen0'text/plain'falsenoendgaps0'text/plain'falsegapext0'text/plain'falsegapdist0'text/plain'falseiteration0'text/plain'falsenumiter0'text/plain'falseclustering0'text/plain'falseoutput0'text/plain'falseoutorder0'text/plain'falsesequence0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="alignment" qname="InputParameters>alignment" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="InputParameters>type" /><s:basetype optional="true" unbounded="false" typename="int" name="ktup" qname="InputParameters>ktup" /><s:basetype optional="true" unbounded="false" typename="int" name="window" qname="InputParameters>window" /><s:basetype optional="true" unbounded="false" typename="string" name="score" qname="InputParameters>score" /><s:basetype optional="true" unbounded="false" typename="int" name="topdiags" qname="InputParameters>topdiags" /><s:basetype optional="true" unbounded="false" typename="int" name="pairgap" qname="InputParameters>pairgap" /><s:basetype optional="true" unbounded="false" typename="string" name="pwmatrix" qname="InputParameters>pwmatrix" /><s:basetype optional="true" unbounded="false" typename="string" name="pwdnamatrix" qname="InputParameters>pwdnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="pwgapopen" qname="InputParameters>pwgapopen" /><s:basetype optional="true" unbounded="false" typename="float" name="pwgapext" qname="InputParameters>pwgapext" /><s:basetype optional="true" unbounded="false" typename="string" name="matrix" qname="InputParameters>matrix" /><s:basetype optional="true" unbounded="false" typename="string" name="dnamatrix" qname="InputParameters>dnamatrix" /><s:basetype optional="true" unbounded="false" typename="int" name="gapopen" qname="InputParameters>gapopen" /><s:basetype optional="true" unbounded="false" typename="boolean" name="noendgaps" qname="InputParameters>noendgaps" /><s:basetype optional="true" unbounded="false" typename="float" name="gapext" qname="InputParameters>gapext" /><s:basetype optional="true" unbounded="false" typename="int" name="gapdist" qname="InputParameters>gapdist" /><s:basetype optional="true" unbounded="false" typename="string" name="iteration" qname="InputParameters>iteration" /><s:basetype optional="true" unbounded="false" typename="int" name="numiter" qname="InputParameters>numiter" /><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters>clustering" /><s:basetype optional="true" unbounded="false" typename="string" name="output" qname="InputParameters>output" /><s:basetype optional="true" unbounded="false" typename="string" name="outorder" qname="InputParameters>outorder" /><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters>sequence" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityoutnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitytreenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId" /><s:basetype optional="false" unbounded="false" typename="string" name="type" qname=">getResult>type" /><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname=">getResult>parameters"><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter>name" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityaln-clustalwnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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>truenet.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputemailrun_inputparametersrun_outputinputrun_input_2sequencegetResultparametersgetResult_inputjobIdgetResult_inputtypegetResult_outputinputgetResult_guideTreeparametersgetResult_tree_inputjobIdgetResult_tree_inputtypegetResult_tree_outputinputgetResult_alignmentparametersgetResult_align_inputjobIdgetResult_align_inputtypegetResult_align_outputinputstatusJobIdClustalW_alignmentClustalW_guide_treeClustalW_outputJob_IDJob_statusEMBL-EBI ClustalW2_SOAP2011-01-17 16:23:03.888 UTC609f649e-b2d6-4163-95c6-1a48a3341b1a2011-01-11 10:16:23.550 UTC24411e27-0652-4739-8d66-0814b5d19afb2013-01-24 15:50:11.485 UTC4cbe4e6c-13d6-4c87-9aea-34bf5cf92aca2013-01-25 09:40:45.881 UTC2f13db4b-d3df-4981-9b0b-d07ebf5c54732011-01-17 16:27:19.878 UTC609f649e-b2d6-4163-95c6-1a48a3341b1a2011-01-11 10:07:49.585 UTCb1606657-3f23-45a7-8730-88a6c13a2e952011-01-11 10:14:51.754 UTCPerform 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 UTCHamish McWilliam, updated by Katy Wolstencroft
2013-01-24 15:48:57.797 UTCclustal_phylogenyalignment00CLUSTAL 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 UTCaccepts a clustalw protein sequence alignment2013-01-24 15:45:54.8 UTCemail00Requires 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 execution2013-01-24 15:32:05.472 UTCstatus_reportgetResult_output_outputrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlrunnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityemail0'text/plain'falsetitle0'text/plain'falseparameters0'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname=">run>email"><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=">run>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=">run>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>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>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>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>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalsejobId0'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=">runResponse>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.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivitytree0'text/plain'falsekimura0'text/plain'falsetossgaps0'text/plain'falseclustering0'text/plain'falsepim0'text/plain'falsesequence0'text/plain'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname=">run>parameters"><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>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>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>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>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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>truenet.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname=">getResult>jobId"><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=">getResult>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=">getResult>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitytreenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'application/octet-stream'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname=">getResultResponse>output"><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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputparametersrun_inputemailrun_outputinputrun_input_2sequencestatusJOB_IDgetResultparametersgetResult_inputtypegetResult_inputjobIdgetResult_outputinputstatus_reportgetResult_output_output5f98399f-4e3a-49c2-90ed-304d619f4b3a2013-01-24 15:32:07.122 UTCc398cdfd-d999-4929-af67-b1d33974649f2013-01-16 13:42:46.931 UTC632445e9-238d-4297-8565-b879c243e5642013-01-16 12:07:31.943 UTCclustal_phylogeny2013-01-16 13:42:34.331 UTCThis 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 UTC651ce628-2792-4cb2-a278-8386d69851ba2013-01-16 13:16:11.852 UTCKaty Wolstencroft2013-01-16 13:42:46.176 UTC1670e09e-294a-4554-85d5-a0c16d5784712013-01-16 13:41:30.191 UTC0dd91d8e-414f-44e1-8840-fa42650c7ce52013-01-16 13:23:52.958 UTC7a509422-a069-41fc-ae01-34d90bd6af552013-01-16 13:11:09.281 UTC443dda04-ff00-466c-9e71-8b133d5cce8a2013-01-16 13:13:45.705 UTC16fd2052-4591-4462-a5a9-5fbce75f4fad2013-01-24 15:46:57.896 UTC6eb99ce5-bc3d-486b-ad2a-d565becd2dbc2013-01-24 15:30:18.916 UTCc647509f-a7fa-41ce-a44d-09e76af4056f2013-01-24 15:31:23.962 UTC56c266b5-970f-4895-94a2-b969dff0917d2013-01-16 13:18:22.999 UTCcfc27e98-1cf9-4d95-a4fe-aec9b5043b232013-01-25 09:44:53.162 UTC8fc02eb6-3912-4487-87bc-ae31ee552bf12013-01-16 13:42:08.616 UTCStatus_jobID00getStatus_output_statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlgetStatusnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falseoutput0'text/xml'0<s:extensions 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qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname=">getStatusResponse>status" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputgetStatus_output_status10b2ab29-e2c4-49ca-8667-2d6185696ac82011-01-11 16:35:36.301 UTC479f5c10-89de-4851-9329-4eca70e743e12011-01-11 16:37:35.2 UTCStatus
2011-01-11 16:37:21.331 UTC