<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> | |
<script>import org.biojava.bio.seq.DNATools; | |
import org.biojava.bio.seq.RNATools; | |
import org.biojava.bio.symbol.SymbolList; | |
if ((dna_seq == void) || (dna_seq == null)) { | |
throw new RuntimeException("The dna_seq must be specified"); | |
} | |
// make a DNA SymbolList | |
SymbolList symL = DNATools.createDNA(dna_seq); | |
// transcribe it to RNA (after BioJava 1.4 this method is | |
// deprecated) | |
symL = RNATools.transcribe(symL); | |
// (after BioJava 1.4 use this method instead) | |
// symL = DNATools.toRNA(symL); | |
// just to prove it worked | |
rna_seq = symL.seqString(); | |
</script> | |
<dependencies class="java.util.Collections$SingletonList"> | |
<element class="string">uk.org.mygrid.resources:biojava:1.4pre1</element> | |
</dependencies> | |
<inputs> | |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> | |
<handledReferenceSchemes /> | |
<translatedElementType>java.lang.String</translatedElementType> | |
<allowsLiteralValues>true</allowsLiteralValues> | |
<name>dna_seq</name> | |
<depth>0</depth> | |
<mimeTypes> | |
<string>'text/plain'</string> | |
</mimeTypes> | |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> | |
</inputs> | |
<outputs> | |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> | |
<granularDepth>0</granularDepth> | |
<name>rna_seq</name> | |
<depth>0</depth> | |
<mimeTypes> | |
<string>'text/plain'</string> | |
</mimeTypes> | |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> | |
</outputs> | |
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean></activity> |