Workflow1source_file00D:\Workflows\Ours\source_proteins.txt2011-03-25 18:35:28.91 GMTsource_id002251846402011-03-25 18:35:35.753 GMTtarget_file00491769662011-03-25 18:34:46.281 GMTD:\Workflows\Ours\target_proteins.txt2011-03-25 18:35:08.986 GMTtarget_id00491769662011-03-25 18:35:15.114 GMTblast_file00finalStatusblasted_identifiersunique_identifiersBlastReportExtract_proteins_using_a_gi___output_as_fasta_file_id1fasta_file_path0file_output11net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_proteins_using_a_gi___output_as_fasta_file__2id1fasta_file_path0file_output11net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_source_urlfasta0url_string00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruefasta0text/plain0url_string0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_target_urlfasta0url_string00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruefasta0text/plain0url_string0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorkflow8subjectURL0queryURL0BlastReport00FinalStatus00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_unique_proteins_from_blast_resultsblastFile0tfasta0blasted_identifiers00unique_identifiers00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_Filefilecontents0outputFile0outputFile00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileWriterworkflowjava.lang.StringtrueoutputFile0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0outputFile0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_proteins_using_a_gi___output_as_fasta_file_idExtract_proteins_using_a_gi___output_as_fasta_file_fasta_file_pathExtract_proteins_using_a_gi___output_as_fasta_file__2idExtract_proteins_using_a_gi___output_as_fasta_file__2fasta_file_pathget_source_urlfastaget_target_urlfastaWorkflow8subjectURLWorkflow8queryURLExtract_unique_proteins_from_blast_resultsblastFileExtract_unique_proteins_from_blast_resultstfastaWrite_Text_FilefilecontentsWrite_Text_FileoutputFilefinalStatusblasted_identifiersunique_identifiersBlastReport2edfb164-cb4d-479a-8d04-d0aa8cc1f08c2011-03-25 18:36:37.159 GMTf3aa632c-a438-4282-8032-71f1b9bf8cbf2011-03-25 18:05:31.610 GMT1014ec4b-5390-4400-95b1-1fde94c708632011-03-25 18:21:53.316 GMT76df289e-a819-48b8-8aed-6e05c2d3ce622011-03-25 19:30:52.803 GMTb2dfccf5-1929-4ce8-9df0-74a3751517de2011-03-25 18:35:46.326 GMTd25f850a-eaab-44b9-b211-03eb448a332b2011-03-25 17:59:40.418 GMTWorkflow3JobID00StatusgetJobStateparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlgetJobStatenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobState" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobState"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getJobState>jobId" /></s:elements></s:complextype></s:extensions>falsejobId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobStateResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobStateResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getJobStateResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobStateparametersgetJobState_inputjobIdgetJobState_outputinputStatusd5767d0c-5a85-4f35-a4fc-8ef5e5bbf60c2011-03-18 12:22:47.500 GMT4e01e2d8-674e-4af5-8df0-317b9ecaa9f22011-03-16 19:37:52.588 GMTc73c43fa-0789-480d-99c8-8207a12fdbaf2011-03-16 17:37:44.858 GMTExtract_unique_proteins_from_blast_resultsblastFile00C:\Users\You2011-03-24 15:20:32.41 GMTThe URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not 2011-03-24 15:20:42.61 GMTThe URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not a file location).2011-03-24 15:20:55.164 GMTC:\Users\You\Documents\my_blast_results.tab2011-03-24 15:21:18.503 GMTinputs the xml format of the blast results2010-03-19 03:21:20.950 GMTThe URL or file path location of the tab-delimited format of the Blast results.2011-03-24 15:20:06.729 GMTtfasta00File : C:\Users\You\Documents\target_fasta.faa2011-03-24 15:22:34.14 GMTFile 2011-03-24 15:21:59.270 GMTfasta file of the target proteins to extract the sequences2010-03-19 03:19:27.444 GMTFasta file of the target proteins to extract the sequences. 2011-03-24 15:21:32.450 GMTFasta file of the target proteins to extract the sequences. Add as file location.2011-03-24 15:21:53.195 GMTunique_identifiersUnique identifiers that appear in the FASTA file but not in the BLAST file. Identifiers are separated by new lines.2011-03-24 15:28:07.208 GMTgi|321313668|ref|YP_004205955.1|
gi|321312432|ref|YP_004204719.1|
gi|321314996|ref|YP_004207283.1|2011-03-24 15:28:18.998 GMTblasted_identifiersIdentifiers of the target genome from the BLAST results. These identifiers are those that are similar to the source proteome.2011-03-24 15:26:18.245 GMTgi|321313668|ref|YP_004205955.1|
gi|321312432|ref|YP_004204719.1|
gi|321314996|ref|YP_004207283.1|2011-03-24 15:27:27.684 GMTRead_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileReaderworkflowjava.lang.Stringtruefileurl0'text/plain'0filecontents0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_unique_proteinsxml_result0gi_lines_val00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruexml_result0text/plain0gi_lines_val0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTfasta_parsergi_val0tfasta_in0cfasta_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruegi_val0text/plainjava.lang.Stringtruetfasta_in0text/plain0cfasta_out0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlExtract_unique_proteinsxml_resultTfasta_parsergi_valTfasta_parsertfasta_inunique_identifiersblasted_identifiersThis workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from).
Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.
Shortcomings:
The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.
All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use.2010-03-15 11:30:59.109 GMT2010-03-19 03:14:00.733 GMTb2579890-b32e-4be4-975b-28659feea68f2011-03-24 13:12:29.54 GMT4d837fd7-5124-4e7c-964b-17de794236cc2011-03-24 15:25:33.719 GMTfetchEnsemblSeqsAndBlast2010-03-15 11:30:59.109 GMTWorkflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome2010-03-19 03:18:26.823 GMTnclteamc2010-03-19 03:15:57.858 GMTThe workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.2010-03-19 03:23:47.653 GMTExtract unique proteins from blast results2010-03-19 03:16:29.89 GMT7045bed3-10bd-4d68-9c66-0135b0ed2dde2011-03-24 15:28:27.232 GMT782c8659-5afb-4518-a8c3-0376a08848162011-03-24 13:52:32.878 GMTBela Tiwari2010-03-15 11:30:59.109 GMTExtract_proteins_using_a_gi___output_as_fasta_file_fasta_file_path00This is where the workflow will save the fasta file2010-03-18 23:57:05.740 GMTid11The workflow uses the gi no to retrieve the xml genbank entry2010-03-18 23:58:02.898 GMTfile_outputprotein output for specified gi in fasta format2010-03-18 23:58:47.780 GMTExtraction_of_infoxml_result0fastas_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruexml_result0text/plain0fastas_out0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_FileoutputFile0filecontents0outputFile00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileWriterworkflowjava.lang.StringtrueoutputFile0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0outputFile0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Nucleotide_GBSeq_XMLid0outputText00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorkerworkflowjava.lang.Stringtrueid0'text/plain'0outputText0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultWrite_Text_FileoutputFileWrite_Text_FilefilecontentsGet_Nucleotide_GBSeq_XMLidfile_output6beeaaf5-900a-438a-8791-76184cbcb4632011-03-24 19:03:54.809 GMTExtract proteins using a gi - output as fasta file 2010-03-18 23:55:22.983 GMTnclteamc2010-03-18 23:54:52.375 GMTThe workflow uses the gi id to retrieve a xml format of the genbank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein fasta file.2010-03-18 23:56:41.809 GMTWorkflow8subjectURL00ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_subtilis_168_uid57675/NC_000964.faa2011-03-25 15:26:55.48 GMTqueryURL00ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_anthracis_Sterne_uid58091/NC_005945.faa2011-03-25 15:28:14.390 GMTftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_anthracis_Sterne_uid58091/NC_005945.faa.2011-03-25 15:27:29.631 GMTJobIDOutputBlastReportFinalStatusaquireSubjectFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlaquireInputFilenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSubjectUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>falseurl0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubjectFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaquireQueryFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlaquireInputFilenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQueryUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>falseurl0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokequeryFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitBlastPJobparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlsubmitBlastPJobnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitBlastPJob_inputsubjectFileId0queryFileId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJob" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJob"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="subjectFileId" qname="submitBlastPJob>subjectFileId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryFileId" qname="submitBlastPJob>queryFileId" /></s:elements></s:complextype></s:extensions>falsesubjectFileId0'text/plain'falsequeryFileId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJobIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJobResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJobResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="submitBlastPJobResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAwaitJobCompletionJobID0Status00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.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 = "" + ! Status.equals("COMPLETED");
if ("true".matches(loop)) {
Thread.sleep(10000);
}</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>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-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReportparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlgetBlastReportnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReport" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReport"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getBlastReport>jobId" /></s:elements></s:complextype></s:extensions>falsejobId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReportResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReportResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getBlastReportResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaquireSubjectFileparametersSubjectUrlInputurlsubjectFileIDinputaquireQueryFileparametersQueryUrlInputurlqueryFileIDinputsubmitBlastPJobparameterssubmitBlastPJob_inputsubjectFileIdsubmitBlastPJob_inputqueryFileIdJobIDinputAwaitJobCompletionJobIDgetBlastReportparametersgetBlastReport_inputjobIdgetBlastReport_outputinputJobIDOutputBlastReportFinalStatusf5981737-10a0-4fc4-9672-3130a03656ab2011-03-16 17:40:41.255 GMT63f00396-c32e-4320-a732-6c682f2464fb2011-03-16 19:07:15.429 GMT01ae999a-1204-42cf-a75a-71d504cd47c72011-03-25 15:28:30.772 GMT00226a02-118c-419e-96df-2dd8869cbfa02011-03-16 16:51:12.261 GMT660f7075-7cd0-4c7c-8240-5ef305e3d0812011-03-16 17:39:20.697 GMTe9287f94-ee6e-483b-8c8b-5284afc5213e2011-03-16 15:34:27.528 GMT5ce9aec8-494f-45dd-a978-3d71564306522011-03-16 14:42:27.305 GMT3b70d4ae-354f-477e-a277-41712da517702011-03-16 17:31:43.390 GMTe0a458bb-2f5c-43e7-b582-745c970a19662011-03-16 17:41:03.200 GMT2a850e45-73b9-4ba8-a782-b7eddd736a6a2011-03-25 15:27:35.782 GMTa2f6d3f7-262b-47b5-9fd1-e191935a19a92011-03-16 17:07:31.320 GMTec74ad83-bc35-4801-9f1a-5895a07707a42011-03-16 17:11:23.916 GMT4d26090f-0bef-4024-ba16-8a69f36909982011-03-16 22:52:59.767 GMT14b5dde3-dfd6-4c04-b254-78c13051998a2011-03-16 19:38:23.32 GMT66e94c9e-a25e-4df1-bcf9-9885484303422011-03-16 14:29:06.933 GMT71ce1c05-e453-4cab-b2e1-ee49bb4534dc2011-03-16 14:28:03.443 GMT573e2324-2806-494a-8127-37eda623cd972011-03-18 11:45:08.987 GMT78ba349d-a426-46bb-b842-57cad76582ef2011-03-18 12:22:51.796 GMTcd88505f-a3f1-4bde-af4a-aa287edf56422011-03-16 17:04:35.157 GMT