taverna-t2flow 0.2.0 → 0.3.0
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- data/CHANGES.rdoc +16 -0
- data/README.rdoc +30 -21
- data/Rakefile +54 -0
- data/lib/t2flow/model.rb +7 -0
- data/lib/t2flow/parser.rb +7 -2
- data/taverna-t2flow.gemspec +76 -0
- data/test/fixtures/1000.t2flow +244 -0
- data/test/fixtures/1001.t2flow +321 -0
- data/test/fixtures/1002.t2flow +474 -0
- data/test/fixtures/1003.t2flow +292 -0
- data/test/fixtures/1004.t2flow +73 -0
- data/test/fixtures/996.t2flow +193 -0
- data/test/fixtures/997.t2flow +359 -0
- data/test/fixtures/998.t2flow +324 -0
- data/test/fixtures/999.t2flow +604 -0
- data/test/fixtures/basic.t2flow +94 -0
- data/test/fixtures/coordinated.t2flow +63 -0
- data/test/fixtures/linked.t2flow +88 -0
- data/test/fixtures/nested.t2flow +270 -0
- data/test/fixtures/processors.t2flow +174 -0
- data/test/run_tests.rb +7 -0
- data/test/test_bogus_workflows.rb +80 -0
- data/test/test_helper.rb +50 -0
- data/test/test_starter_pack_workflows.rb +132 -0
- metadata +121 -69
- data/ChangeLog.rdoc +0 -7
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="2f216461-50f5-45be-a2d2-49c84b1fce5e" role="top"><name>BiomartAndEMBOSSAnalysis</name><inputPorts /><outputPorts><port><name>outputPlot</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationAssertions>
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.MimeType">
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<text>image/png</text>
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<date>2009-12-15 21:49:47.668 GMT</date>
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<creators />
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<date>2009-12-15 21:49:47.668 GMT</date>
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>HSapIDs</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.MimeType">
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<text>text/plain</text>
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</annotationBean>
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<date>2009-12-15 21:49:47.668 GMT</date>
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>MMusIDs</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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</annotationBean>
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<date>2009-12-15 21:49:47.668 GMT</date>
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>RNorIDs</name><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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<annotationAssertions>
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.MimeType">
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</annotationBean>
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<date>2009-12-15 21:49:47.668 GMT</date>
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<creators />
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<curationEventList />
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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</annotationAssertions>
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</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></outputPorts><processors><processor><name>GetUniqueHomolog</name><inputPorts><port><name>HSGeneIDs</name><depth>1</depth></port><port><name>RatGeneIDs</name><depth>1</depth></port><port><name>MouseGeneIDs</name><depth>1</depth></port></inputPorts><outputPorts><port><name>MouseOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>HSOut</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>RatOut</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="RatGeneIDs" to="RatGeneIDs" /><map from="HSGeneIDs" to="HSGeneIDs" /><map from="MouseGeneIDs" to="MouseGeneIDs" /></inputMap><outputMap><map from="RatOut" to="RatOut" /><map from="HSOut" to="HSOut" /><map from="MouseOut" to="MouseOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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<script>List HSOut = new ArrayList();
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List RatOut = new ArrayList();
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List MouseOut = new ArrayList();
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Map hsToMouse = new HashMap();
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Iterator j = MouseGeneIDs.iterator();
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for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
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String id = (String)i.next();
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hsToMouse.put(id, j.next());
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}
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Map hsToRat = new HashMap();
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j = RatGeneIDs.iterator();
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for (Iterator i = HSGeneIDs.iterator(); i.hasNext();) {
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String id = (String)i.next();
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hsToRat.put(id, j.next());
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}
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// Build the unique outputs
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for (Iterator i = hsToRat.keySet().iterator(); i.hasNext();) {
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String hsID = (String)i.next();
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String ratID = (String)hsToRat.get(hsID);
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// Remove version number
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// ratID = (ratID.split("."))[0];
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String mouseID = (String)hsToMouse.get(hsID);
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// Remove version number
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//mouseId = (mouseID.split("."))[0];
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if (ratID != null && mouseID != null && ratID.equals("")==false && mouseID.equals("")==false) {
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HSOut.add(hsID);
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RatOut.add(ratID.split("\\.")[0]);
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MouseOut.add(mouseID.split("\\.")[0]);
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}
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}</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>HSGeneIDs</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>MouseGeneIDs</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>RatGeneIDs</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>1</granularDepth>
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<name>HSOut</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>1</granularDepth>
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<name>RatOut</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>1</granularDepth>
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<name>MouseOut</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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<maxJobs>1</maxJobs>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>0</initialDelay>
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="RatGeneIDs" depth="1" /><port name="MouseGeneIDs" depth="1" /><port name="HSGeneIDs" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>hsapiensGeneEnsembl</name><inputPorts /><outputPorts><port><name>hsapiens_gene_ensembl.mouse_ensembl_gene</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_gene_ensembl.rat_ensembl_gene</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap /><outputMap><map from="hsapiens_gene_ensembl.rat_ensembl_gene" to="hsapiens_gene_ensembl.rat_ensembl_gene" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /><map from="hsapiens_gene_ensembl.mouse_ensembl_gene" to="hsapiens_gene_ensembl.mouse_ensembl_gene" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:24:08"><MartURLLocation database="ensembl_mart_55" default="1" displayName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna"><Dataset name="hsapiens_gene_ensembl"><Attribute name="ensembl_gene_id" /><Attribute name="mouse_ensembl_gene" /><Attribute name="rat_ensembl_gene" /><Filter name="chromosome_name" value="22" /><Filter name="with_mmusculus_homolog" excluded="0" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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<maxJobs>1</maxJobs>
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>0</initialDelay>
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<maxDelay>0</maxDelay>
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<maxRetries>0</maxRetries>
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</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><dot><port name="hsSeq" depth="0" /><port name="mmSeq" depth="0" /><port name="rnSeq" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>getRNorSequence</name><inputPorts><port><name>rnorvegicus_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>rnorvegicus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>rnorvegicus_gene_ensembl.coding_gene_flank</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap><map from="rnorvegicus_gene_ensembl.ensembl_gene_id_filter" to="rnorvegicus_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="rnorvegicus_gene_ensembl.coding_gene_flank" to="rnorvegicus_gene_ensembl.coding_gene_flank" /><map from="rnorvegicus_gene_ensembl.ensembl_gene_id" to="rnorvegicus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Rattus norvegicus genes (RGSC3.4)" name="rnorvegicus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:36:01"><MartURLLocation database="ensembl_mart_55" default="1" displayName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna"><Dataset name="rnorvegicus_gene_ensembl"><Attribute name="coding_gene_flank" /><Attribute name="ensembl_gene_id" /><Filter name="ensembl_gene_id" value="" list="true" /><Filter name="upstream_flank" value="100" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="rnorvegicus_gene_ensembl.ensembl_gene_id_filter" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>getMMusSequence</name><inputPorts><port><name>mmusculus_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>mmusculus_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>mmusculus_gene_ensembl.coding_gene_flank</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomart-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.biomart.BiomartActivity</class><inputMap><map from="mmusculus_gene_ensembl.ensembl_gene_id_filter" to="mmusculus_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="mmusculus_gene_ensembl.coding_gene_flank" to="mmusculus_gene_ensembl.coding_gene_flank" /><map from="mmusculus_gene_ensembl.ensembl_gene_id" to="mmusculus_gene_ensembl.ensembl_gene_id" /></outputMap><configBean encoding="jdomxml"><MartQuery xmlns=""><MartService location="http://www.biomart.org/biomart/martservice" /><MartDataset displayName="Mus musculus genes (NCBIM37)" name="mmusculus_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2009-07-15 14:45:36"><MartURLLocation database="ensembl_mart_55" default="1" displayName="ENSEMBL 55 GENES (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" /></MartDataset><Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna"><Dataset name="mmusculus_gene_ensembl"><Attribute name="coding_gene_flank" /><Attribute name="ensembl_gene_id" /><Filter name="ensembl_gene_id" value="" list="true" /><Filter name="upstream_flank" value="100" /></Dataset></Query></MartQuery></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
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</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
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<script>flatten(inputs, outputs, depth) {
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for (i = inputs.iterator(); i.hasNext();) {
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element = i.next();
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flatten(element, outputs, depth - 1);
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} else {
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outputs.add(element);
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}
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}
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}
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outputlist = new ArrayList();
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flatten(inputlist, outputlist, 1);</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>[B</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>inputlist</name>
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<depth>2</depth>
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<mimeTypes>
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<string>l(l(''))</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<granularDepth>1</granularDepth>
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<name>outputlist</name>
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<depth>1</depth>
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<string>l('')</string>
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</mimeTypes>
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<text>BiomartAndEMBOSSAnalysis</text>
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<date>2009-12-15 21:49:49.57 GMT</date>
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<text>Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.</text>
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<date>2009-12-15 21:49:49.57 GMT</date>
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<text />
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<date>2009-12-15 21:49:49.57 GMT</date>
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