Workflow1source_file00 D:\Workflows\Ours\source_proteins.txt 2011-03-25 18:35:28.91 GMT source_id00 225184640 2011-03-25 18:35:35.753 GMT target_file00 49176966 2011-03-25 18:34:46.281 GMT D:\Workflows\Ours\target_proteins.txt 2011-03-25 18:35:08.986 GMT target_id00 49176966 2011-03-25 18:35:15.114 GMT blast_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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true fasta 0 text/plain 0 url_string 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true fasta 0 text/plain 0 url_string 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileWriter workflow java.lang.String true outputFile 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 outputFile 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_proteins_using_a_gi___output_as_fasta_file_idsource_idExtract_proteins_using_a_gi___output_as_fasta_file_fasta_file_pathsource_fileExtract_proteins_using_a_gi___output_as_fasta_file__2idtarget_idExtract_proteins_using_a_gi___output_as_fasta_file__2fasta_file_pathtarget_fileget_source_urlfastaExtract_proteins_using_a_gi___output_as_fasta_file_file_outputget_target_urlfastaExtract_proteins_using_a_gi___output_as_fasta_file__2file_outputWorkflow8subjectURLget_source_urlurl_stringWorkflow8queryURLget_target_urlurl_stringExtract_unique_proteins_from_blast_resultsblastFileblast_fileExtract_unique_proteins_from_blast_resultstfastaExtract_proteins_using_a_gi___output_as_fasta_file__2file_outputWrite_Text_FilefilecontentsWorkflow8BlastReportWrite_Text_FileoutputFileblast_filefinalStatusWorkflow8FinalStatusblasted_identifiersExtract_unique_proteins_from_blast_resultsblasted_identifiersunique_identifiersExtract_unique_proteins_from_blast_resultsunique_identifiersBlastReportWrite_Text_FileoutputFile 2edfb164-cb4d-479a-8d04-d0aa8cc1f08c 2011-03-25 18:36:37.159 GMT f3aa632c-a438-4282-8032-71f1b9bf8cbf 2011-03-25 18:05:31.610 GMT 1014ec4b-5390-4400-95b1-1fde94c70863 2011-03-25 18:21:53.316 GMT 76df289e-a819-48b8-8aed-6e05c2d3ce62 2011-03-25 19:30:52.803 GMT b2dfccf5-1929-4ce8-9df0-74a3751517de 2011-03-25 18:35:46.326 GMT d25f850a-eaab-44b9-b211-03eb448a332b 2011-03-25 17:59:40.418 GMT Workflow3JobID00StatusgetJobStateparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl getJobState net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;jobId" /></s:elements></s:complextype></s:extensions> false jobId 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;return" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobStateparametersgetJobState_inputoutputgetJobState_inputjobIdJobIDgetJobState_outputinputgetJobStateparametersStatusgetJobState_outputreturn d5767d0c-5a85-4f35-a4fc-8ef5e5bbf60c 2011-03-18 12:22:47.500 GMT 4e01e2d8-674e-4af5-8df0-317b9ecaa9f2 2011-03-16 19:37:52.588 GMT c73c43fa-0789-480d-99c8-8207a12fdbaf 2011-03-16 17:37:44.858 GMT Extract_unique_proteins_from_blast_resultsblastFile00 C:\Users\You 2011-03-24 15:20:32.41 GMT The 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 GMT The 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 GMT C:\Users\You\Documents\my_blast_results.tab 2011-03-24 15:21:18.503 GMT inputs the xml format of the blast results 2010-03-19 03:21:20.950 GMT The URL or file path location of the tab-delimited format of the Blast results. 2011-03-24 15:20:06.729 GMT tfasta00 File : C:\Users\You\Documents\target_fasta.faa 2011-03-24 15:22:34.14 GMT File 2011-03-24 15:21:59.270 GMT fasta file of the target proteins to extract the sequences 2010-03-19 03:19:27.444 GMT Fasta file of the target proteins to extract the sequences. 2011-03-24 15:21:32.450 GMT Fasta file of the target proteins to extract the sequences. Add as file location. 2011-03-24 15:21:53.195 GMT unique_identifiers Unique 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 GMT gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:28:18.998 GMT blasted_identifiers Identifiers 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 GMT gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:27:27.684 GMT Read_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true xml_result 0 text/plain 0 gi_lines_val 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true gi_val 0 text/plain java.lang.String true tfasta_in 0 text/plain 0 cfasta_out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlblastFileExtract_unique_proteinsxml_resultRead_Text_FilefilecontentsTfasta_parsergi_valExtract_unique_proteinsgi_lines_valTfasta_parsertfasta_intfastaunique_identifiersTfasta_parsercfasta_outblasted_identifiersExtract_unique_proteinsgi_lines_val This 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 GMT 2010-03-19 03:14:00.733 GMT b2579890-b32e-4be4-975b-28659feea68f 2011-03-24 13:12:29.54 GMT 4d837fd7-5124-4e7c-964b-17de794236cc 2011-03-24 15:25:33.719 GMT fetchEnsemblSeqsAndBlast 2010-03-15 11:30:59.109 GMT Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome 2010-03-19 03:18:26.823 GMT nclteamc 2010-03-19 03:15:57.858 GMT The 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 GMT Extract unique proteins from blast results 2010-03-19 03:16:29.89 GMT 7045bed3-10bd-4d68-9c66-0135b0ed2dde 2011-03-24 15:28:27.232 GMT 782c8659-5afb-4518-a8c3-0376a0884816 2011-03-24 13:52:32.878 GMT Bela Tiwari 2010-03-15 11:30:59.109 GMT Extract_proteins_using_a_gi___output_as_fasta_file_fasta_file_path00 This is where the workflow will save the fasta file 2010-03-18 23:57:05.740 GMT id11 The workflow uses the gi no to retrieve the xml genbank entry 2010-03-18 23:58:02.898 GMT file_output protein output for specified gi in fasta format 2010-03-18 23:58:47.780 GMT Extraction_of_infoxml_result0fastas_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true xml_result 0 text/plain 0 fastas_out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileWriter workflow java.lang.String true outputFile 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 outputFile 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker workflow java.lang.String true id 0 'text/plain' 0 outputText 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultGet_Nucleotide_GBSeq_XMLoutputTextWrite_Text_FileoutputFilefasta_file_pathWrite_Text_FilefilecontentsExtraction_of_infofastas_outGet_Nucleotide_GBSeq_XMLididfile_outputWrite_Text_FileoutputFile 6beeaaf5-900a-438a-8791-76184cbcb463 2011-03-24 19:03:54.809 GMT Extract proteins using a gi - output as fasta file 2010-03-18 23:55:22.983 GMT nclteamc 2010-03-18 23:54:52.375 GMT The 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 GMT Workflow8subjectURL00 ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_subtilis_168_uid57675/NC_000964.faa 2011-03-25 15:26:55.48 GMT queryURL00 ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_anthracis_Sterne_uid58091/NC_005945.faa 2011-03-25 15:28:14.390 GMT ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bacillus_anthracis_Sterne_uid58091/NC_005945.faa. 2011-03-25 15:27:29.631 GMT JobIDOutputBlastReportFinalStatusaquireSubjectFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl aquireInputFile net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;url" /></s:elements></s:complextype></s:extensions> false url 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;return" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl aquireInputFile net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;url" /></s:elements></s:complextype></s:extensions> false url 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;return" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl submitBlastPJob net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;subjectFileId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryFileId" qname="submitBlastPJob&gt;queryFileId" /></s:elements></s:complextype></s:extensions> false subjectFileId 0 'text/plain' false queryFileId 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;return" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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> true net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl getBlastReport net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;jobId" /></s:elements></s:complextype></s:extensions> false jobId 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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&gt;return" /></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaquireSubjectFileparametersSubjectUrlInputoutputSubjectUrlInputurlsubjectURLsubjectFileIDinputaquireSubjectFileparametersaquireQueryFileparametersQueryUrlInputoutputQueryUrlInputurlqueryURLqueryFileIDinputaquireQueryFileparameterssubmitBlastPJobparameterssubmitBlastPJob_inputoutputsubmitBlastPJob_inputsubjectFileIdsubjectFileIDreturnsubmitBlastPJob_inputqueryFileIdqueryFileIDreturnJobIDinputsubmitBlastPJobparametersAwaitJobCompletionJobIDJobIDreturngetBlastReportparametersgetBlastReport_inputoutputgetBlastReport_inputjobIdJobIDreturngetBlastReport_outputinputgetBlastReportparametersJobIDOutputJobIDreturnBlastReportgetBlastReport_outputreturnFinalStatusAwaitJobCompletionStatus f5981737-10a0-4fc4-9672-3130a03656ab 2011-03-16 17:40:41.255 GMT 63f00396-c32e-4320-a732-6c682f2464fb 2011-03-16 19:07:15.429 GMT 01ae999a-1204-42cf-a75a-71d504cd47c7 2011-03-25 15:28:30.772 GMT 00226a02-118c-419e-96df-2dd8869cbfa0 2011-03-16 16:51:12.261 GMT 660f7075-7cd0-4c7c-8240-5ef305e3d081 2011-03-16 17:39:20.697 GMT e9287f94-ee6e-483b-8c8b-5284afc5213e 2011-03-16 15:34:27.528 GMT 5ce9aec8-494f-45dd-a978-3d7156430652 2011-03-16 14:42:27.305 GMT 3b70d4ae-354f-477e-a277-41712da51770 2011-03-16 17:31:43.390 GMT e0a458bb-2f5c-43e7-b582-745c970a1966 2011-03-16 17:41:03.200 GMT 2a850e45-73b9-4ba8-a782-b7eddd736a6a 2011-03-25 15:27:35.782 GMT a2f6d3f7-262b-47b5-9fd1-e191935a19a9 2011-03-16 17:07:31.320 GMT ec74ad83-bc35-4801-9f1a-5895a07707a4 2011-03-16 17:11:23.916 GMT 4d26090f-0bef-4024-ba16-8a69f3690998 2011-03-16 22:52:59.767 GMT 14b5dde3-dfd6-4c04-b254-78c13051998a 2011-03-16 19:38:23.32 GMT 66e94c9e-a25e-4df1-bcf9-988548430342 2011-03-16 14:29:06.933 GMT 71ce1c05-e453-4cab-b2e1-ee49bb4534dc 2011-03-16 14:28:03.443 GMT 573e2324-2806-494a-8127-37eda623cd97 2011-03-18 11:45:08.987 GMT 78ba349d-a426-46bb-b842-57cad76582ef 2011-03-18 12:22:51.796 GMT cd88505f-a3f1-4bde-af4a-aa287edf5642 2011-03-16 17:04:35.157 GMT