--- a
+++ b/test/resources/sshTool.t2flow
@@ -0,0 +1,108 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="93971f50-9f59-4f71-adc7-f08f5a5eb53a" role="top"><name>Workflow1</name><inputPorts><port><name>input</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>output</name><annotations /></port></outputPorts><processors><processor><name>Tool</name><inputPorts><port><name>in1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>STDOUT</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="in1" to="in1" /></inputMap><outputMap><map from="STDOUT" to="STDOUT" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
+ <mechanismType>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
+ <mechanismName>fuel</mechanismName>
+ <mechanismXML><?xml version="1.0" encoding="UTF-8"?>
+<sshInvocation><sshNode><host>fue.onb.ac.at</host><port>22</port><directory>/tmp/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
+</mechanismXML>
+ <externaltoolid>e1195d09-0d9c-4e19-9971-490f6a9f8984</externaltoolid>
+ <useCaseDescription>
+ <usecaseid />
+ <description />
+ <command>C:\Users\munterberger\workspace\TavernaExtractor\test\resources\tool.bat %%in1%%</command>
+ <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
+ <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
+ <tags>
+ <string>in1</string>
+ </tags>
+ <REs />
+ <queue__preferred />
+ <queue__deny />
+ <static__inputs />
+ <inputs>
+ <entry>
+ <string>in1</string>
+ <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ <tag>in1</tag>
+ <file>false</file>
+ <tempFile>false</tempFile>
+ <binary>false</binary>
+ <charsetName>windows-1252</charsetName>
+ <forceCopy>false</forceCopy>
+ <list>false</list>
+ <concatenate>false</concatenate>
+ <mime />
+ </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+ </entry>
+ </inputs>
+ <outputs />
+ <includeStdIn>false</includeStdIn>
+ <includeStdOut>true</includeStdOut>
+ <includeStdErr>true</includeStdErr>
+ <validReturnCodes>
+ <int>0</int>
+ </validReturnCodes>
+ </useCaseDescription>
+ <edited>false</edited>
+</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="">
+ <maxJobs>1</maxJobs>
+</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>1.4</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>1.4</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>1.4</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="">
+ <backoffFactor>1.0</backoffFactor>
+ <initialDelay>1000</initialDelay>
+ <maxDelay>5000</maxDelay>
+ <maxRetries>0</maxRetries>
+</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>1.4</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="in1" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>in1</port></sink><source type="dataflow"><port>input</port></source></datalink><datalink><sink type="dataflow"><port>output</port></sink><source type="processor"><processor>Tool</processor><port>STDOUT</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>93971f50-9f59-4f71-adc7-f08f5a5eb53a</identification>
+ </annotationBean>
+ <date>2014-01-23 12:01:02.140 UTC</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>97fd16b3-d09d-470b-bf2c-e7067aa37512</identification>
+ </annotationBean>
+ <date>2014-01-23 09:10:39.610 UTC</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>39d27bf9-8e12-4e65-b37e-f08df2c0f328</identification>
+ </annotationBean>
+ <date>2014-01-23 09:37:59.465 UTC</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>ccea8ae7-8f22-4467-960b-f4acae5252f8</identification>
+ </annotationBean>
+ <date>2014-01-23 09:48:54.544 UTC</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+ <annotationAssertions>
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+ <identification>22849d21-1657-4e98-bf0c-ce332554f8c5</identification>
+ </annotationBean>
+ <date>2014-01-23 09:47:51.845 UTC</date>
+ <creators />
+ <curationEventList />
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+ </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>