taverna-t2flow 0.2.0 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -0,0 +1,359 @@
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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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+ </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><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>application/octet-stream</text>
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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><port><name>HSapIDs</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>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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+ <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><port><name>MMusIDs</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>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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+ <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><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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+ <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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+ <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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+
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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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+
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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 &amp;&amp; mouseID != null &amp;&amp; ratID.equals("")==false &amp;&amp; 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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+ </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>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.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 /></strategy></iteration></iterationStrategyStack></processor><processor><name>getHSapSequence</name><inputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id_filter</name><depth>1</depth></port></inputPorts><outputPorts><port><name>hsapiens_gene_ensembl.ensembl_gene_id</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>hsapiens_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="hsapiens_gene_ensembl.ensembl_gene_id_filter" to="hsapiens_gene_ensembl.ensembl_gene_id_filter" /></inputMap><outputMap><map from="hsapiens_gene_ensembl.coding_gene_flank" to="hsapiens_gene_ensembl.coding_gene_flank" /><map from="hsapiens_gene_ensembl.ensembl_gene_id" to="hsapiens_gene_ensembl.ensembl_gene_id" /></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="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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+ <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="hsapiens_gene_ensembl.ensembl_gene_id_filter" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CreateFasta</name><inputPorts><port><name>hsSeq</name><depth>0</depth></port><port><name>rnSeq</name><depth>0</depth></port><port><name>mmSeq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fasta</name><depth>0</depth><granularDepth>0</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="hsSeq" to="hsSeq" /><map from="rnSeq" to="rnSeq" /><map from="mmSeq" to="mmSeq" /></inputMap><outputMap><map from="fasta" to="fasta" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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+ <script>fasta = "&gt;Human\n"+hsSeq+"\n&gt;Mouse\n"+mmSeq+"\n&gt;Rat\n"+rnSeq;</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>hsSeq</name>
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+ <depth>0</depth>
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+ <mimeTypes>
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+ <string>'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>mmSeq</name>
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+ <depth>0</depth>
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+ <mimeTypes>
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+ <string>'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>rnSeq</name>
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+ <depth>0</depth>
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+ <mimeTypes>
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+ <string>'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>0</granularDepth>
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+ <name>fasta</name>
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+ <depth>0</depth>
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+ <mimeTypes>
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+ <string>'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>
222
+ </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="">
223
+ <backoffFactor>1.0</backoffFactor>
224
+ <initialDelay>0</initialDelay>
225
+ <maxDelay>0</maxDelay>
226
+ <maxRetries>0</maxRetries>
227
+ </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="">
228
+ <maxJobs>1</maxJobs>
229
+ </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="">
230
+ <backoffFactor>1.0</backoffFactor>
231
+ <initialDelay>0</initialDelay>
232
+ <maxDelay>0</maxDelay>
233
+ <maxRetries>0</maxRetries>
234
+ </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="">
235
+ <maxJobs>1</maxJobs>
236
+ </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="">
237
+ <backoffFactor>1.0</backoffFactor>
238
+ <initialDelay>0</initialDelay>
239
+ <maxDelay>0</maxDelay>
240
+ <maxRetries>0</maxRetries>
241
+ </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="mmusculus_gene_ensembl.ensembl_gene_id_filter" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>FlattenImageList</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
242
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>
243
+ <script>flatten(inputs, outputs, depth) {
244
+ for (i = inputs.iterator(); i.hasNext();) {
245
+ element = i.next();
246
+ if (element instanceof Collection &amp;&amp; depth &gt; 0) {
247
+ flatten(element, outputs, depth - 1);
248
+ } else {
249
+ outputs.add(element);
250
+ }
251
+ }
252
+ }
253
+
254
+ outputlist = new ArrayList();
255
+
256
+ flatten(inputlist, outputlist, 1);</script>
257
+ <dependencies />
258
+ <classLoaderSharing>workflow</classLoaderSharing>
259
+ <localDependencies />
260
+ <artifactDependencies />
261
+ <inputs>
262
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
263
+ <handledReferenceSchemes />
264
+ <translatedElementType>[B</translatedElementType>
265
+ <allowsLiteralValues>true</allowsLiteralValues>
266
+ <name>inputlist</name>
267
+ <depth>2</depth>
268
+ <mimeTypes>
269
+ <string>l(l(''))</string>
270
+ </mimeTypes>
271
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
272
+ </inputs>
273
+ <outputs>
274
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
275
+ <granularDepth>1</granularDepth>
276
+ <name>outputlist</name>
277
+ <depth>1</depth>
278
+ <mimeTypes>
279
+ <string>l('')</string>
280
+ </mimeTypes>
281
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
282
+ </outputs>
283
+ </net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></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="">
284
+ <maxJobs>1</maxJobs>
285
+ </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="">
286
+ <backoffFactor>1.0</backoffFactor>
287
+ <initialDelay>0</initialDelay>
288
+ <maxDelay>0</maxDelay>
289
+ <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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>seqret</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outseq_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outseq_url" to="outseq_url" /><map from="report" to="report" /><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
291
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret</endpoint>
292
+ <pollingInterval>0</pollingInterval>
293
+ <pollingBackoff>1.0</pollingBackoff>
294
+ <pollingIntervalMax>0</pollingIntervalMax>
295
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></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="">
296
+ <maxJobs>5</maxJobs>
297
+ </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="">
298
+ <backoffFactor>1.0</backoffFactor>
299
+ <initialDelay>0</initialDelay>
300
+ <maxDelay>0</maxDelay>
301
+ <maxRetries>0</maxRetries>
302
+ </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="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>plot</name><inputPorts><port><name>sequences_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Graphics_in_Postscript_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>Graphics_in_Postscript</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>Graphics_in_PNG</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>Graphics_in_PNG_url</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequences_direct_data" to="sequences_direct_data" /></inputMap><outputMap><map from="Graphics_in_PNG_url" to="Graphics_in_PNG_url" /><map from="Graphics_in_Postscript_url" to="Graphics_in_Postscript_url" /><map from="Graphics_in_Postscript" to="Graphics_in_Postscript" /><map from="report" to="report" /><map from="Graphics_in_PNG" to="Graphics_in_PNG" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
303
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot</endpoint>
304
+ <pollingInterval>0</pollingInterval>
305
+ <pollingBackoff>1.0</pollingBackoff>
306
+ <pollingIntervalMax>0</pollingIntervalMax>
307
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></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="">
308
+ <maxJobs>5</maxJobs>
309
+ </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="">
310
+ <backoffFactor>1.0</backoffFactor>
311
+ <initialDelay>0</initialDelay>
312
+ <maxDelay>0</maxDelay>
313
+ <maxRetries>0</maxRetries>
314
+ </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="sequences_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>emma</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>dendoutfile_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>dendoutfile</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>outseq_url</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>report</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outseq_url" to="outseq_url" /><map from="dendoutfile" to="dendoutfile" /><map from="dendoutfile_url" to="dendoutfile_url" /><map from="report" to="report" /><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
315
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma</endpoint>
316
+ <pollingInterval>0</pollingInterval>
317
+ <pollingBackoff>1.0</pollingBackoff>
318
+ <pollingIntervalMax>0</pollingIntervalMax>
319
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></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="">
320
+ <maxJobs>5</maxJobs>
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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="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>HSGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.ensembl_gene_id</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>RatGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.rat_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>GetUniqueHomolog</processor><port>MouseGeneIDs</port></sink><source type="processor"><processor>hsapiensGeneEnsembl</processor><port>hsapiens_gene_ensembl.mouse_ensembl_gene</port></source></datalink><datalink><sink type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>hsSeq</port></sink><source type="processor"><processor>getHSapSequence</processor><port>hsapiens_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>rnSeq</port></sink><source type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>CreateFasta</processor><port>mmSeq</port></sink><source type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.coding_gene_flank</port></source></datalink><datalink><sink type="processor"><processor>getRNorSequence</processor><port>rnorvegicus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</port></source></datalink><datalink><sink type="processor"><processor>getMMusSequence</processor><port>mmusculus_gene_ensembl.ensembl_gene_id_filter</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</port></source></datalink><datalink><sink type="processor"><processor>FlattenImageList</processor><port>inputlist</port></sink><source type="processor"><processor>plot</processor><port>Graphics_in_PNG</port></source></datalink><datalink><sink type="processor"><processor>seqret</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>CreateFasta</processor><port>fasta</port></source></datalink><datalink><sink type="processor"><processor>plot</processor><port>sequences_direct_data</port></sink><source type="processor"><processor>emma</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>emma</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink><datalink><sink type="dataflow"><port>outputPlot</port></sink><source type="processor"><processor>FlattenImageList</processor><port>outputlist</port></source></datalink><datalink><sink type="dataflow"><port>HSapIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>HSOut</port></source></datalink><datalink><sink type="dataflow"><port>MMusIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>MouseOut</port></source></datalink><datalink><sink type="dataflow"><port>RNorIDs</port></sink><source type="processor"><processor>GetUniqueHomolog</processor><port>RatOut</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
327
+ <annotationAssertions>
328
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
329
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
330
+ <text>BiomartAndEMBOSSAnalysis</text>
331
+ </annotationBean>
332
+ <date>2009-12-15 21:49:49.57 GMT</date>
333
+ <creators />
334
+ <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><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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+ <annotationAssertions>
339
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
340
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
341
+ <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>
342
+ </annotationBean>
343
+ <date>2009-12-15 21:49:49.57 GMT</date>
344
+ <creators />
345
+ <curationEventList />
346
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
347
+ </annotationAssertions>
348
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
349
+ <annotationAssertions>
350
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
351
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
352
+ <text />
353
+ </annotationBean>
354
+ <date>2009-12-15 21:49:49.57 GMT</date>
355
+ <creators />
356
+ <curationEventList />
357
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
358
+ </annotationAssertions>
359
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>