Define_Associated_Regions_and_Genesparameters00
Parameter XML Document
2011-06-03 09:18:42.976 BST
<Parameters>
<Parameter name="associatedSNPs"><AsociatedSNPs>
<AssociatedSNP rsId="rs6920220" pValue="1.08E-15"/>
</AsociatedSNPs></Parameter>
</Parameters>
2011-06-03 09:19:54.811 BST
associatedRegionsXML
Output XML Document
2011-06-03 09:20:12.970 BST
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseParametersxpathparseParametersparamXMLget_SNPsSNPListmakeLiftOverParamsDbSnpToHapMapassociatedSNPmakeLiftOverParamsDbSnpToHapMapfromBuildmakeLiftOverParamsDbSnpToHapMaptoBuilddbSnpToHapMapChainfromBuilddbSnpToHapMapChaintoBuildliftoverdbSnpToHapMapparametersliftoverdbSnpToHapMapchainXMLunifyHapmapBuildbuildInaddLDRegionassociatedSNPaddLDRegionhapmapBuildaddLDRegionflankingKBaddLDRegionpopaddLDRegionhapmapVersionaddLDRegionplugindefineLDRegionassociatedSNPdefineLDRegionbaseURLdefineLDRegionrsqCutoffHapMapToHotspotChaintoBuildHapMapToHotspotChainfromBuildmakeLiftOverParamsHapMapToHotspottoBuildmakeLiftOverParamsHapMapToHotspotfromBuildmakeLiftOverParamsHapMapToHotspotassociatedSNPliftoverHapMapToHotspotparametersliftoverHapMapToHotspotchainXMLgetHotspotRegionsassociatedSnpHotspotToHg18ChainfromBuildHotspotToHg18ChaintoBuildHotspotToEnsemblChainfromBuildHotspotToEnsemblChaintoBuildmakeLiftOverParamsHotspotToHg18associatedSNPmakeLiftOverParamsHotspotToHg18toBuildmakeLiftOverParamsHotspotToHg18fromBuildliftoverHotspotToHg18parametersliftoverHotspotToHg18chainXMLmakeLiftOverParamsHotspotToEnsemblfromBuildmakeLiftOverParamsHotspotToEnsemblassociatedSNPmakeLiftOverParamsHotspotToEnsembltoBuildliftoverHotspotToEnsemblchainXMLliftoverHotspotToEnsemblparametersgetAssociatedGenesensemblBiomartBuildgetAssociatedGenesAssociatedXMLgetAssociatedGenesdatasetgetAssociatedGenesvirtualSchemagetAssociatedGenesbaseUrlmergeResultsxmlResultsmakeLiftOverParamsHapMapToEnsembltoBuildmakeLiftOverParamsHapMapToEnsemblassociatedSNPmakeLiftOverParamsHapMapToEnsemblfromBuildliftoverHapMapToEnsemblparametersliftoverHapMapToEnsemblchainXMLHapMapToEnsemblChaintoBuildHapMapToEnsemblChainfromBuildgetEnsemblInfobaseUrlassociatedRegionsXML
Paul Martin
2010-06-21 13:48:39.740 BST
f7eee9ae-ec59-419c-85ac-bdf0c62e47f1
2012-01-24 10:31:48.782 GMT
3ddbe5fb-b731-424e-9b17-fd5928100932
2011-10-07 13:25:31.640 BST
8f1e3083-ca63-4634-859a-89d07a356093
2011-10-07 13:43:17.839 BST
ec54a14c-13bc-4ae0-85c4-e16e2b01ebe1
2011-10-07 12:54:07.476 BST
Defines regions and genes from associated SNPs
2010-06-21 13:49:43.255 BST
b6c5ce01-76af-4b2c-a786-27fd8ac37af8
2011-10-07 12:24:20.118 BST
Define Associated Regions and Genes
2010-06-21 13:49:18.948 BST
b7f497b8-7928-4110-990e-5682aebe78e0
2011-10-07 13:48:51.586 BST
87b5c895-7cb1-4669-80a5-541444e90594
2012-01-24 11:06:49.958 GMT
30583d85-9bc3-4c6f-a242-596ab9b7093a
2011-10-07 13:37:01.444 BST
Define_LD_RegionassociatedSNP00baseURL00rsqCutoff00AssociatedSNPOutgetLDByRegionbaseURL0associatedSNP0rsqCutoffString0associatedSnpOut00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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UserNameHere
2010-12-09 12:24:25.426 GMT
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseHapMapDataassocSNP0rsqCutoffString0assocSNPout00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetLDByRegionbaseURLgetLDByRegionassociatedSNPgetLDByRegionrsqCutoffStringparseHapMapDataassocSNPparseHapMapDatarsqCutoffStringAssociatedSNPOut
Define LD Region
2010-02-17 13:12:39.135 GMT
Paul Martin
2010-02-17 13:12:05.186 GMT
c11abb19-7024-4ad7-9891-e368426588e2
2011-10-07 12:24:21.349 BST
Workflow141queries11virtualSchema00dataset00baseUrl00biomartResponsebuildXMLQueriesdataset0virtualSchema0queries1xmlQueries11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebiomartQueryURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBiomartResponsequery0url0biomartResponse11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateUrlstring20string10output00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebuildXMLQueriesdatasetbuildXMLQueriesvirtualSchemabuildXMLQueriesqueriesgetBiomartResponsequerygetBiomartResponseurlflattenBiomartResponseinputlistcreateUrlstring2createUrlstring1biomartResponse
cd4b10fe-ee1b-410f-aa56-aa5153a1606c
2011-10-07 13:25:01.99 BST
068d6dbe-9489-4164-ac16-bc1a0e4e9587
2012-01-24 10:30:44.473 GMT
5ce77ae4-42f5-48fd-b510-4163d4a3be18
2011-10-07 12:18:06.756 BST
Workflow60AssociatedXML00ensemblBiomartBuild00dataset00virtualSchema00baseUrl00AssociatedXmlOutputgetAssociatedRegionLocationsassociatedXML0ensemblBiomartBuild0queries11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBiomartResponsequeries1virtualSchema0dataset0baseUrl0biomartResponse11net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetAssociatedRegionLocationsassociatedXMLgetAssociatedRegionLocationsensemblBiomartBuildcreateGeneXMLensemblBiomartBuildcreateGeneXMLbiomartResultsArrayaddGenesToAssociatedXMLgeneXMLaddGenesToAssociatedXMLassociatedXmlInaddGenesToAssociatedXMLensemblBiomartBuildgetBiomartResponsequeriesgetBiomartResponsevirtualSchemagetBiomartResponsedatasetgetBiomartResponsebaseUrlAssociatedXmlOutput
73a6f7f2-aac3-4afc-ae68-ff06a6188299
2011-10-07 13:42:35.744 BST
bf6bee48-be7a-4990-ad1a-cb39b03bae03
2011-10-07 13:48:47.717 BST
09530105-23d0-4bb7-81da-3151db9af74e
2011-10-07 12:23:49.453 BST
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2011-10-07 13:25:05.809 BST
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2011-10-07 12:18:06.680 BST
173d6f11-5142-42f7-bbb2-c70dabd640e9
2012-01-24 10:30:52.897 GMT
626e6950-b84d-4bc9-98a0-8530e2666bcd
2011-10-07 13:36:16.677 BST
Unify_Genome_BuildbuildIn00ucscBuildOutncbiBuildOuterrorunifyBuildbuildIn0errorString00ncbiBuildOut00ucscBuildOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeunifyBuildbuildInucscBuildOutncbiBuildOuterror
Given a build string attempts to produce the build representation for NCBI/Ensembl and UCSC.
2010-04-08 13:26:17.937 BST
b38d97b8-95ba-4edf-bde9-40ac98f699e4
2011-10-07 12:24:20.806 BST
Unify Genome Build
2010-04-08 13:16:52.598 BST
Paul Martin
2010-04-08 13:16:33.575 BST
Convert_Genomic_Co_ordinatesparameters00chainXML00xmlOutliftOvercontiguous0minMatch0xmlIn0nodesToConvert0chainXmlString0xmlOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeliftOvercontiguousliftOverminMatchliftOverxmlInliftOvernodesToConvertliftOverchainXmlStringparseParametersparamXMLxmlOut
8cf4b155-da34-4076-967e-ecf59b5aca2a
2011-10-07 12:24:21.52 BST
Paul Martin
2010-04-26 16:00:57.252 BST
bbc18262-5e1e-45b4-b94e-bfdd572fbd88
2011-10-07 13:21:52.924 BST
Converts genomic co-ordinates between builds for the same species. Requires XML Locations as input.
2010-04-26 16:02:30.153 BST
Convert Genomic Co-ordinates
2010-04-26 16:01:35.910 BST
Convert_Genomic_Co_ordinatesparameters00chainXML00xmlOutliftOvercontiguous0minMatch0xmlIn0nodesToConvert0chainXmlString0xmlOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
xmlIn
0
text/plain
java.lang.String
true
contiguous
0
text/plain
java.lang.String
true
minMatch
0
text/plain
java.lang.String
true
chainXmlString
0
text/plain
java.lang.String
true
nodesToConvert
0
text/plain
java.lang.String
true
xmlOut
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseParametersparamXML0contiguous00minMatch00xmlIn00rootNode00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
paramXML
0
'text/xml'
java.lang.String
true
toBuild
0
0
fromBuild
0
0
xmlIn
0
0
contiguous
0
0
minMatch
0
0
rootNode
0
0
workflow
dom4j:dom4j:1.6
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
UserNameHere
2010-05-05 16:53:22.183 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeliftOvercontiguousliftOverminMatchliftOverxmlInliftOvernodesToConvertliftOverchainXmlStringparseParametersparamXMLxmlOut
e03e4fbb-32e5-460a-9c9d-c2986040dc6c
2011-10-07 12:24:21.216 BST
Converts genomic co-ordinates between builds for the same species. Requires XML Locations as input.
2010-04-26 16:02:30.153 BST
Convert Genomic Co-ordinates
2010-04-26 16:01:35.910 BST
Paul Martin
2010-04-26 16:00:57.252 BST
Workflow109datasetvirtualSchemahapmartRegistryURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
http://hapmap.ncbi.nlm.nih.gov/biomart/martservice?type=registry
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokehapmartDatasetURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
http://hapmap.ncbi.nlm.nih.gov/biomart/martservice?type=datasets&mart=
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHapMartRegistryurl0name00virtualSchema00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
0
'text/x-taverna-web-url'
java.lang.String
true
virtualSchema
0
0
name
0
0
workflow
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
UserNameHere
2010-11-11 11:14:35.90 GMT
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokejoinHapMartDatasetURLstring20string10output00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string1
0
'text/plain'
java.lang.String
true
string2
0
'text/plain'
java.lang.String
true
output
0
'text/plain'
0
workflow
org.embl.ebi.escience.scuflworkers.java.StringConcat
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokedownloadHapMartDatasetsurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
0
'text/x-taverna-web-url'
java.lang.String
true
base
0
'text/x-taverna-web-url'
java.lang.String
true
contents
0
'text/plain,text/html'
0
workflow
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHapMartDatasethapmartDatasets0dataset00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
hapmartDatasets
0
'text/plain'
java.lang.String
true
dataset
0
0
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
UserNameHere
2010-11-12 09:56:17.638 GMT
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHapMartRegistryurljoinHapMartDatasetURLstring2joinHapMartDatasetURLstring1downloadHapMartDatasetsurlgetHapMartDatasethapmartDatasetsdatasetvirtualSchema
33838205-a676-4300-af63-813e22b5df37
2011-10-07 12:24:21.130 BST
Convert_UCSC_liftover_chain_file_to_XMLfromBuild00toBuild00chainXMLgetChainUrlsurlTemplate0fromBuild0toBuild0chainUrls11chainConversions11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
urlTemplate
0
text/plain
java.lang.String
true
fromBuild
0
text/plain
java.lang.String
true
toBuild
0
text/plain
java.lang.String
true
chainUrls
1
1
chainConversions
1
1
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeurlTemplatevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
http://hgdownload.cse.ucsc.edu/goldenPath/%s/liftOver/%sTo%s.over.chain.gz
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetChainXmlchainUrls1chainConversions1fromBuild0toBuild0chainXml00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
chainUrls
1
text/plain
java.lang.String
true
chainConversions
1
text/plain
java.lang.String
true
fromBuild
0
text/plain
java.lang.String
true
toBuild
0
text/plain
java.lang.String
true
chainXml
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetChainUrlsurlTemplategetChainUrlsfromBuildgetChainUrlstoBuildgetChainXmlchainUrlsgetChainXmlchainConversionsgetChainXmlfromBuildgetChainXmltoBuildchainXML
Given a conversion type (e.g. hg19 to hg18), downloads the relevant chain file(s) from UCSC and processes to XML.
2010-04-08 12:46:00.748 BST
Convert UCSC liftover chain file to XML
2010-04-08 12:44:39.294 BST
ce8b5b59-bfd8-47c5-9653-42e60b7fe42d
2011-10-07 12:24:20.756 BST
Paul Martin
2010-04-08 12:43:52.528 BST
Unify_Genome_BuildbuildIn00ucscBuildOutncbiBuildOuterrorunifyBuildbuildIn0errorString00ncbiBuildOut00ucscBuildOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
buildIn
0
text/plain
java.lang.String
true
ncbiBuildOut
0
0
errorString
0
0
ucscBuildOut
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeunifyBuildbuildInucscBuildOutncbiBuildOuterror
Unify Genome Build
2010-04-08 13:16:52.598 BST
Given a build string attempts to produce the build representation for NCBI/Ensembl and UCSC.
2010-04-08 13:26:17.937 BST
Paul Martin
2010-04-08 13:16:33.575 BST
684355e4-d805-4d18-b123-4f534539d66b
2011-10-07 12:24:20.829 BST
Convert_Genomic_Co_ordinatesparameters00chainXML00xmlOutliftOvercontiguous0minMatch0xmlIn0nodesToConvert0chainXmlString0xmlOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
xmlIn
0
text/plain
java.lang.String
true
contiguous
0
text/plain
java.lang.String
true
minMatch
0
text/plain
java.lang.String
true
chainXmlString
0
text/plain
java.lang.String
true
nodesToConvert
0
text/plain
java.lang.String
true
xmlOut
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseParametersparamXML0contiguous00minMatch00xmlIn00rootNode00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
paramXML
0
'text/xml'
java.lang.String
true
toBuild
0
0
fromBuild
0
0
xmlIn
0
0
contiguous
0
0
minMatch
0
0
rootNode
0
0
workflow
dom4j:dom4j:1.6
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
UserNameHere
2010-05-05 16:53:22.183 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeliftOvercontiguousliftOverminMatchliftOverxmlInliftOvernodesToConvertliftOverchainXmlStringparseParametersparamXMLxmlOut
Paul Martin
2010-04-26 16:00:57.252 BST
Convert Genomic Co-ordinates
2010-04-26 16:01:35.910 BST
3ce3fd14-5b92-4fe6-8198-bba08b46242d
2011-10-07 12:24:20.478 BST
Converts genomic co-ordinates between builds for the same species. Requires XML Locations as input.
2010-04-26 16:02:30.153 BST
gets_associated_SNP_info_from_NCBISNPList11
2010-01-22 13:26:27.843 GMT
text/plain
2010-01-22 13:26:27.796 GMT
output
text/xml
2010-01-22 13:26:27.859 GMT
buildeUtilsDBvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
snp
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeremoveDuplicateSNPsassociatedSNPs1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
associatedSNPs
1
l('text/plain')
java.lang.String
true
strippedlist
1
1
workflow
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
UserNameHere
2010-04-28 16:33:59.106 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeeFetchXMLdb0id0output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
db
0
'text/plain'
java.lang.String
true
id
0
'text/plain'
java.lang.String
true
WebEnv
0
'text/plain'
java.lang.String
true
query_key
0
'text/plain'
java.lang.String
true
tool
0
'text/plain'
java.lang.String
true
email
0
'text/plain'
java.lang.String
true
retstart
0
'text/plain'
java.lang.String
true
retmax
0
'text/plain'
java.lang.String
true
rettype
0
'text/plain'
java.lang.String
true
strand
0
'text/plain'
java.lang.String
true
seq_start
0
'text/plain'
java.lang.String
true
seq_stop
0
'text/plain'
java.lang.String
true
complexity
0
'text/plain'
java.lang.String
true
report
0
'text/plain'
java.lang.String
true
output
0
'text/xml'
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefetchSNPsparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
run_eFetch
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetRsXMLxpath0xml-text0nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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java.lang.String
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1
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dom4j
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716010169
dom4j:dom4j:1.6
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokersPathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
/*[local-name(.)='eFetchResult']/*[local-name(.)='ExchangeSet']/*[local-name(.)='Rs']
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTransform_XMLinFileURL0xslFileURL0outputStr00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
xslFileURL
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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2
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_and_populate_XML_filecontent0filePath00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
content
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filePath
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1
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1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeflattenSNPsinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
inputlist
2
l(l(''))
[B
true
outputlist
1
l('')
1
workflow
org.embl.ebi.escience.scuflworkers.java.FlattenList
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemergeXMLdbSNP1snpXML1xmlOut11rsIds11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
dbSNP
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snpXML
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddHapMapAttributesnpXML1hapmapSNPs1snpXMLOut11dbSnpBuild00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
snpXML
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hapmapSNPs
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateRsXslfilePath00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
filePath
0
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1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHapMartInfodataset00virtualSchema00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecheckHapMapdataset0virtualSchema0rsIds1hapmapRsIds11net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeremoveDuplicateSNPsassociatedSNPseFetchXMLdbeFetchXMLidfetchSNPsparametersgetRsXMLxpathgetRsXMLxml-textTransform_XMLinFileURLTransform_XMLxslFileURLCreate_and_populate_XML_filecontentflattenSNPsinputlistmergeXMLdbSNPmergeXMLsnpXMLaddHapMapAttributesnpXMLaddHapMapAttributehapmapSNPscheckHapMapdatasetcheckHapMapvirtualSchemacheckHapMaprsIdsoutputbuild
2010-01-22 13:26:31.265 GMT
7ce1555c-38cf-48e9-aafd-49c201204347
2011-10-07 12:24:20.566 BST
Paul Martin
2010-01-22 13:26:31.265 GMT
5b7cc1d3-6e9c-49df-b19e-872bdeba068d
2012-01-24 10:31:33.961 GMT
gets associated SNP info from NCBI
2010-02-17 12:17:27.734 GMT
Workflow27baseUrl00datasetschemagetEnsemblInforegistryXML0baseUrl0schemaOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
registryXML
0
text/plain
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baseUrl
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schemaOut
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1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetRegistryurl0base0contents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
0
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0
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java.lang.String
true
contents
0
'text/plain,text/html'
0
workflow
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetRegistryURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
/biomart/martservice?type=registry
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetDatasetsurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
0
'text/x-taverna-web-url'
java.lang.String
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base
0
'text/x-taverna-web-url'
java.lang.String
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contents
0
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0
workflow
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetDatasetdatasets0dataset00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
datasets
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1.0
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefinishDatasetUrlbaseUrl0url00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
baseUrl
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url
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEnsemblInforegistryXMLgetEnsemblInfobaseUrlgetRegistryurlgetRegistrybasegetDatasetsurlgetDatasetdatasetsfinishDatasetUrlbaseUrldatasetschema
9e1f1b3f-b222-409e-9882-9a58c8d5ac02
2011-10-07 12:24:20.977 BST
Workflow119rsIds11dataset00virtualSchema00hapmapRsIdshapmartQueryURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
http://hapmap.ncbi.nlm.nih.gov/biomart/martservice
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1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebuildXMLQueriesvirtualSchema0dataset0rsIds1xmlQueries11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
rsIds
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1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHapMartResponseurl0query0hapmapRsId11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
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1
1
workflow
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
UserNameHere
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeflattenHapMapRsIdsinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
inputlist
2
l(l(''))
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outputlist
1
l('')
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org.embl.ebi.escience.scuflworkers.java.FlattenList
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebuildXMLQueriesvirtualSchemabuildXMLQueriesdatasetbuildXMLQueriesrsIdsgetHapMartResponseurlgetHapMartResponsequeryflattenHapMapRsIdsinputlisthapmapRsIds
f3b56dff-5fb9-4ecd-a7fd-34cac88cae6c
2011-10-07 12:24:20.425 BST
cdfa8c3b-8e12-4e91-bed6-cbf331ea9c29
2012-01-24 10:31:14.929 GMT
Convert_Genomic_Co_ordinatesparameters00chainXML00xmlOutliftOvercontiguous0minMatch0xmlIn0nodesToConvert0chainXmlString0xmlOut00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparseParametersparamXML0contiguous00minMatch00xmlIn00rootNode00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
paramXML
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dom4j:dom4j:1.6
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
UserNameHere
2010-05-05 16:53:22.183 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeliftOvercontiguousliftOverminMatchliftOverxmlInliftOvernodesToConvertliftOverchainXmlStringparseParametersparamXMLxmlOut
Convert Genomic Co-ordinates
2010-04-26 16:01:35.910 BST
cd4d2d50-1ab7-4f8d-960f-cc0647bd3e89
2011-10-07 12:24:21.91 BST
Paul Martin
2010-04-26 16:00:57.252 BST
Converts genomic co-ordinates between builds for the same species. Requires XML Locations as input.
2010-04-26 16:02:30.153 BST
Workflow19associatedSnp00outgetRecombinationHotspotsdriver0url0userid0hapmap5sql0hapmap3sql0perlegen5sql0perlegen3sql0associatedSnpXML0associatedSNPOut00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
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hapmap3sql
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perlegen5sql
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perlegen3sql
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associatedSnpXML
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true
associatedSNPOut
0
0
workflow
net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
UserNameHere
2010-12-10 09:36:13.997 GMT
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedrivervalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
com.mysql.jdbc.Driver
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeurlvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
jdbc:mysql://genome-mysql.cse.ucsc.edu:3306/hg17
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genome
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SELECT chromStart, chromEnd FROM snpRecombHotspotHapmap WHERE chrom = ? AND chromEnd <= ? ORDER BY chromEnd DESC LIMIT 1
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SELECT chromStart, chromEnd FROM snpRecombHotspotHapmap WHERE chrom = ? AND chromStart >= ? ORDER BY chromStart ASC LIMIT 1
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPerlegenHotspots5_SQLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
SELECT chromStart, chromEnd FROM snpRecombHotspotPerlegen WHERE chrom = ? AND chromEnd <= ? ORDER BY chromEnd DESC LIMIT 1
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPerlegenHotspots3_SQLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
SELECT chromStart, chromEnd FROM snpRecombHotspotPerlegen WHERE chrom = ? AND chromStart >= ? ORDER BY chromStart ASC LIMIT 1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetRecombinationHotspotsdrivergetRecombinationHotspotsurlgetRecombinationHotspotsuseridgetRecombinationHotspotshapmap5sqlgetRecombinationHotspotshapmap3sqlgetRecombinationHotspotsperlegen5sqlgetRecombinationHotspotsperlegen3sqlgetRecombinationHotspotsassociatedSnpXMLout
3e68e183-ce8e-4ade-86d7-01cde22fb9a9
2011-10-07 12:24:21.256 BST
Workflow60ucscBuildgetEnsemblBiomartDatasetsurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity
url
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeensemblBiomartQueryURLvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetHumanBuildFromDatasetsbiomartResponse0ncbiBuild00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity
biomartResponse
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ncbiBuild
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokencbiBuildToUcscbuildIn0ucscBuildOut00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEnsemblBiomartDatasetsurlgetHumanBuildFromDatasetsbiomartResponsencbiBuildToUcscbuildInucscBuild
85e82a59-ba77-4af6-bb08-f70f37a00415
2011-10-07 12:24:20.520 BST