Associated_Region_to_Gene_ListadditionalParameters00 Allows the user to supply any additional parameters. Options are:- nameType [associatedName, ensgId, ucscId, description] addRsId [false, true] addPvalue [false, true] geneStatus [null, anyGeneStatus] excludeHLA [false, true] The first value in each list specifies the default value for that parameter. HLA region is defined as 28477797-3344854, based on genome assembly hg19/GRCh37. 2011-10-10 10:37:25.135 BST nameType ensgId addPvalue true 2011-10-10 09:03:30.415 BST associatedSNPs00 <AssociatedSNPs> <AssociatedSNP pValue="0.00E+00" rsId="rs660895"> <SnpInfo rsId="660895" isHapMap="true" dbSnpBuild="134"> <Created>83</Created> <Updated>132</Updated> <Sequence> <Seq5>CTTGGGAGGCT...AAAAACAAGACTTGTAT</Seq5> <Observed>A/G</Observed> <Seq3>GCTATAGATGGA...TTGTCTCCAGCAG</Seq3> </Sequence> 2011-10-10 09:10:16.288 BST AssociatedSNPs XML document 2011-10-10 09:07:13.299 BST errorsgeneNamesparseParametersxpath0paramXML0errorsIn1associatedSNPs11addPvalue00nameType00errorsOut11geneStatus00excludeHLA00addRsId00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity paramXML 0 text/plain java.lang.String true xpath 0 text/plain java.lang.String true errorsIn 1 text/plain java.lang.String true nameType 0 0 addPvalue 0 0 associatedSNPs 1 1 errorsOut 1 1 geneStatus 0 0 excludeHLA 0 0 addRsId 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.InvokeassociatedSnpXpathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity */AssociatedSNP 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.InvokegetGeneNamesassociatedSNPs1addPvalue0nameType0geneStatus0excludeHLA0addRsId0geneNames11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity nameType 0 text/plain java.lang.String true associatedSNPs 1 text/plain java.lang.String true addPvalue 0 text/plain java.lang.String true geneStatus 0 text/plain java.lang.String true excludeHLA 0 text/plain java.lang.String true addRsId 0 text/plain java.lang.String true geneNames 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.InvokeaddAssociatedParameterassociatedSNPs0paramXML00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity associatedSNPs 0 text/plain java.lang.String true paramXML 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.InvokeadditionalParamsToListstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.3net.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.InvokeaddAdditionalParamsadditionalParams1paramXmlIn0paramXmlOut00errors11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity additionalParams 1 text/plain java.lang.String true paramXmlIn 0 text/plain java.lang.String true paramXmlOut 0 0 errors 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.InvokesplitParamsRegexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [\n\r]+ 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.InvokeremoveDuplicateGenesstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true strippedlist 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates 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.InvokegeneListToStringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity stringlist 1 l('text/plain') java.lang.String true seperator 0 'text/plain' java.lang.String true concatenated 0 'text/plain' 0 workflow org.embl.ebi.escience.scuflworkers.java.StringListMerge net.sf.taverna.t2.coreworkflowmodel-impl1.3net.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.InvokeparseParametersxpathassociatedSnpXpathvalueparseParametersparamXMLaddAdditionalParamsparamXmlOutparseParameterserrorsInaddAdditionalParamserrorsgetGeneNamesassociatedSNPsparseParametersassociatedSNPsgetGeneNamesaddPvalueparseParametersaddPvaluegetGeneNamesnameTypeparseParametersnameTypegetGeneNamesgeneStatusparseParametersgeneStatusgetGeneNamesexcludeHLAparseParametersexcludeHLAgetGeneNamesaddRsIdparseParametersaddRsIdaddAssociatedParameterassociatedSNPsassociatedSNPsadditionalParamsToListstringadditionalParametersadditionalParamsToListregexsplitParamsRegexvalueaddAdditionalParamsadditionalParamsadditionalParamsToListsplitaddAdditionalParamsparamXmlInaddAssociatedParameterparamXMLremoveDuplicateGenesstringlistgetGeneNamesgeneNamesgeneListToStringstringlistremoveDuplicateGenesstrippedlisterrorsparseParameterserrorsOutgeneNamesgeneListToStringconcatenated a7d303ab-a8e7-4cdb-87a9-7a5adb55b481 2011-10-10 09:00:59.182 BST ecaeb556-a306-4e11-90d4-bc9d96c84d63 2011-10-10 09:07:00.652 BST Paul Martin 2011-10-10 09:01:21.341 BST b8f36f06-5b73-4234-990a-5002c1ba5b79 2011-10-10 10:37:27.719 BST Produces a gene list from the Associated Region XML file 2011-10-10 09:02:20.669 BST Associated Region to Gene List 2011-10-10 09:01:48.677 BST 78a95e6a-6f62-413f-8bec-000ef7b58665 2011-10-10 09:02:20.868 BST 3b33fa73-9cb0-44f5-a750-a195ba3ada47 2011-10-10 09:10:16.444 BST