<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.2" log="0">
  <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:afcb8402-7cee-421c-881c-040b9a8c84b7" author="" title="being_done" />
  <s:processor name="Decode_base64_to_byte">
    <s:local>org.embl.ebi.escience.scuflworkers.java.DecodeBase64</s:local>
  </s:processor>
  <s:processor name="runGFF2JPEG">
    <s:description>Runs gff2ps software to vizualize a set of GFF annotations maps. It returns an encoded image in JPEG format.</s:description>
    <s:biomobywsdl>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>runGFF2JPEG</s:serviceName>
      <s:authorityName>genome.imim.es</s:authorityName>
    </s:biomobywsdl>
  </s:processor>
  <s:processor name="runGeneIDGFF">
    <s:description>Ab initio gene prediction tool that returns the gene predictions in GFF format (GFF version 2).</s:description>
    <s:biomobywsdl>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>runGeneIDGFF</s:serviceName>
      <s:authorityName>genome.imim.es</s:authorityName>
      <s:Parameter s:name="strand">Both</s:Parameter>
      <s:Parameter s:name="profile">Homo sapiens (suitable for mammals)</s:Parameter>
      <s:Parameter s:name="engine">Normal</s:Parameter>
      <s:Parameter s:name="signals">None</s:Parameter>
      <s:Parameter s:name="exons">None</s:Parameter>
    </s:biomobywsdl>
  </s:processor>
  <s:processor name="fromFASTAToDNASequence">
    <s:description>Converts a DNA FASTA sequence into a DNA sequence</s:description>
    <s:biomobywsdl>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>fromFASTAToDNASequence</s:serviceName>
      <s:authorityName>genome.imim.es</s:authorityName>
    </s:biomobywsdl>
  </s:processor>
  <s:processor name="String">
    <s:description>a string</s:description>
    <s:biomobyobject>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>String</s:serviceName>
      <s:authorityName />
    </s:biomobyobject>
  </s:processor>
  <s:processor name="Parse_Moby_Data_GFF">
    <s:description>Processor to parse the datatype GFF</s:description>
    <s:biomobyparser>
      <s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
      <s:datatype>GFF</s:datatype>
      <s:articleName>geneid_predictions</s:articleName>
      <s:description>Processor to parse the datatype GFF</s:description>
    </s:biomobyparser>
  </s:processor>
  <s:processor name="Parse_Moby_Data_b64_encoded_jpeg">
    <s:description>Processor to parse the datatype b64_encoded_jpeg</s:description>
    <s:biomobyparser>
      <s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
      <s:datatype>b64_encoded_jpeg</s:datatype>
      <s:articleName>image</s:articleName>
      <s:description>Processor to parse the datatype b64_encoded_jpeg</s:description>
    </s:biomobyparser>
  </s:processor>
  <s:processor name="FASTA_NA">
    <s:description>NA sequence in FASTA format</s:description>
    <s:biomobyobject>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>FASTA_NA</s:serviceName>
      <s:authorityName />
    </s:biomobyobject>
  </s:processor>
  <s:link source="Decode_base64_to_byte:bytes" sink="gff_map" />
  <s:link source="FASTA_NA:mobyData" sink="fromFASTAToDNASequence:FASTA_NA(sequence)" />
  <s:link source="Parse_Moby_Data_b64_encoded_jpeg:image_'content'" sink="Decode_base64_to_byte:base64" />
  <s:link source="String:mobyData" sink="FASTA_NA:String(content)" />
  <s:link source="fromFASTAToDNASequence:DNASequence(sequence)" sink="runGeneIDGFF:DNASequence(sequence)" />
  <s:link source="sequence" sink="String:value" />
  <s:link source="runGFF2JPEG:b64_encoded_jpeg(image)" sink="Parse_Moby_Data_b64_encoded_jpeg:mobyData('b64_encoded_jpeg')" />
  <s:link source="runGeneIDGFF:GFF(geneid_predictions)" sink="Parse_Moby_Data_GFF:mobyData('GFF')" />
  <s:link source="runGeneIDGFF:GFF(geneid_predictions)" sink="runGFF2JPEG:GFF(Collection - 'maps')" />
  <s:link source="Parse_Moby_Data_GFF:geneid_predictions_'content'" sink="geneid_predictions" />
  <s:source name="sequence" />
  <s:sink name="geneid_predictions" />
  <s:sink name="gff_map">
    <s:metadata>
      <s:mimeTypes>
        <s:mimeType>image/*</s:mimeType>
      </s:mimeTypes>
    </s:metadata>
  </s:sink>
</s:scufl>


