<?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:b9e6f797-10d4-4c08-8a1b-e8574749f98a" author="" title="RNAmmer" />
  <s:processor name="RNAmmer">
    <s:arbitrarywsdl>
      <s:wsdl>http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_1a.wsdl</s:wsdl>
      <s:operation>runService</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="getSeq">
    <s:arbitrarywsdl>
      <s:wsdl>http://www.cbs.dtu.dk/ws/GenomeAtlas/GenomeAtlas_3_0.wsdl</s:wsdl>
      <s:operation>getSeq</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="getSeqIn1">
    <s:defaults>
      <s:default name="parameters" />
    </s:defaults>
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="getSeq" name="parameters" qname="{http://www.cbs.dtu.dk/ws/WSGenomeAtlas_3_0}getSeq">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;getSeq&gt;parameters" name="parameters" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;getSeq&gt;parameters">
              <s:elements>
                <s:complextype optional="false" unbounded="false" typename="&gt;&gt;getSeq&gt;parameters&gt;accession" name="accession" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;&gt;getSeq&gt;parameters&gt;accession">
                  <s:elements>
                    <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                  </s:elements>
                </s:complextype>
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="getSeqIn2">
    <s:defaults>
      <s:default name="accession" />
    </s:defaults>
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="&gt;getSeq&gt;parameters" name="parameters" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;getSeq&gt;parameters">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;&gt;getSeq&gt;parameters&gt;accession" name="accession" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;&gt;getSeq&gt;parameters&gt;accession">
              <s:elements>
                <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="getSeqOut1">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="getSeqResponse" name="parameters" qname="{http://www.cbs.dtu.dk/ws/WSGenomeAtlas_3_0}getSeqResponse">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;getSeqResponse&gt;output" name="output" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;getSeqResponse&gt;output">
              <s:elements>
                <s:arraytype optional="false" unbounded="false" typename="sequences" name="sequences" qname="{http://www.cbs.dtu.dk/ws/ws-common}sequences">
                  <s:elementtype>
                    <s:complextype optional="false" unbounded="false" typename="&gt;sequences&gt;entry" name="" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;sequences&gt;entry">
                      <s:elements>
                        <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;ident" name="ident" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;ident">
                          <s:elements>
                            <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                          </s:elements>
                        </s:complextype>
                        <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;seq" name="seq" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;seq">
                          <s:elements>
                            <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                          </s:elements>
                        </s:complextype>
                      </s:elements>
                    </s:complextype>
                  </s:elementtype>
                </s:arraytype>
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="getSeqOut2">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="&gt;getSeqResponse&gt;output" name="output" qname="{http://www.cbs.dtu.dk/ws/ws-genomeatlas}&gt;getSeqResponse&gt;output">
          <s:elements>
            <s:arraytype optional="false" unbounded="false" typename="sequences" name="sequences" qname="{http://www.cbs.dtu.dk/ws/ws-common}sequences">
              <s:elementtype>
                <s:complextype optional="false" unbounded="false" typename="&gt;sequences&gt;entry" name="" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;sequences&gt;entry">
                  <s:elements>
                    <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;ident" name="ident" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;ident">
                      <s:elements>
                        <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                      </s:elements>
                    </s:complextype>
                    <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;seq" name="seq" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;seq">
                      <s:elements>
                        <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                      </s:elements>
                    </s:complextype>
                  </s:elements>
                </s:complextype>
              </s:elementtype>
            </s:arraytype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="RNAmmerIn1">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="runService" name="parameters" qname="{http://www.cbs.dtu.dk/ws/WSRNAmmer_1_1a}runService">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;runService&gt;parameters" name="parameters" qname="{http://www.cbs.dtu.dk/ws/ws-rnammer}&gt;runService&gt;parameters">
              <s:elements>
                <s:complextype optional="false" unbounded="false" typename="&gt;&gt;runService&gt;parameters&gt;kingdom" name="kingdom" qname="{http://www.cbs.dtu.dk/ws/ws-rnammer}&gt;&gt;runService&gt;parameters&gt;kingdom">
                  <s:elements>
                    <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                  </s:elements>
                </s:complextype>
                <s:arraytype optional="false" unbounded="false" typename="sequences" name="sequences" qname="{http://www.cbs.dtu.dk/ws/ws-common}sequences">
                  <s:elementtype>
                    <s:complextype optional="false" unbounded="false" typename="&gt;sequences&gt;entry" name="" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;sequences&gt;entry">
                      <s:elements>
                        <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;ident" name="ident" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;ident">
                          <s:elements>
                            <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                          </s:elements>
                        </s:complextype>
                        <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;seq" name="seq" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;seq">
                          <s:elements>
                            <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                          </s:elements>
                        </s:complextype>
                      </s:elements>
                    </s:complextype>
                  </s:elementtype>
                </s:arraytype>
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="RNAmmerIn2">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="&gt;runService&gt;parameters" name="parameters" qname="{http://www.cbs.dtu.dk/ws/ws-rnammer}&gt;runService&gt;parameters">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;&gt;runService&gt;parameters&gt;kingdom" name="kingdom" qname="{http://www.cbs.dtu.dk/ws/ws-rnammer}&gt;&gt;runService&gt;parameters&gt;kingdom">
              <s:elements>
                <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
              </s:elements>
            </s:complextype>
            <s:arraytype optional="false" unbounded="false" typename="sequences" name="sequences" qname="{http://www.cbs.dtu.dk/ws/ws-common}sequences">
              <s:elementtype>
                <s:complextype optional="false" unbounded="false" typename="&gt;sequences&gt;entry" name="" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;sequences&gt;entry">
                  <s:elements>
                    <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;ident" name="ident" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;ident">
                      <s:elements>
                        <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                      </s:elements>
                    </s:complextype>
                    <s:complextype optional="false" unbounded="false" typename="&gt;&gt;sequences&gt;entry&gt;seq" name="seq" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;&gt;sequences&gt;entry&gt;seq">
                      <s:elements>
                        <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                      </s:elements>
                    </s:complextype>
                  </s:elements>
                </s:complextype>
              </s:elementtype>
            </s:arraytype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="Kingdom" boring="true">
    <s:stringconstant>&lt;kingdom&gt;bac&lt;/kingdom&gt;</s:stringconstant>
  </s:processor>
  <s:processor name="RNAmmerOut1">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="runServiceResponse" name="parameters" qname="{http://www.cbs.dtu.dk/ws/WSRNAmmer_1_1a}runServiceResponse">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="&gt;runServiceResponse&gt;queueentry" name="queueentry" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;runServiceResponse&gt;queueentry">
              <s:elements>
                <s:complextype optional="false" unbounded="false" typename="jobid" name="jobid" qname="{http://www.cbs.dtu.dk/ws/ws-common}jobid">
                  <s:elements>
                    <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                  </s:elements>
                </s:complextype>
                <s:complextype optional="false" unbounded="false" typename="datetime" name="datetime" qname="{http://www.cbs.dtu.dk/ws/ws-common}datetime">
                  <s:elements>
                    <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                  </s:elements>
                </s:complextype>
                <s:complextype optional="false" unbounded="false" typename="jobstatus" name="status" qname="{http://www.cbs.dtu.dk/ws/ws-common}jobstatus">
                  <s:elements>
                    <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
                  </s:elements>
                </s:complextype>
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="RNAmmerOut2">
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="&gt;runServiceResponse&gt;queueentry" name="queueentry" qname="{http://www.cbs.dtu.dk/ws/ws-common}&gt;runServiceResponse&gt;queueentry">
          <s:elements>
            <s:complextype optional="false" unbounded="false" typename="jobid" name="jobid" qname="{http://www.cbs.dtu.dk/ws/ws-common}jobid">
              <s:elements>
                <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
              </s:elements>
            </s:complextype>
            <s:complextype optional="false" unbounded="false" typename="datetime" name="datetime" qname="{http://www.cbs.dtu.dk/ws/ws-common}datetime">
              <s:elements>
                <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
              </s:elements>
            </s:complextype>
            <s:complextype optional="false" unbounded="false" typename="jobstatus" name="status" qname="{http://www.cbs.dtu.dk/ws/ws-common}jobstatus">
              <s:elements>
                <s:basetype optional="false" unbounded="false" typename="string" name="value" qname="{http://www.w3.org/2001/XMLSchema}string" />
              </s:elements>
            </s:complextype>
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:link source="accession" sink="getSeqIn2:accession" />
  <s:link source="Kingdom:value" sink="RNAmmerIn2:kingdom" />
  <s:link source="RNAmmer:parameters" sink="RNAmmerOut1:input" />
  <s:link source="RNAmmerIn1:output" sink="RNAmmer:parameters" />
  <s:link source="RNAmmerIn2:output" sink="RNAmmerIn1:parameters" />
  <s:link source="RNAmmerOut1:queueentry" sink="RNAmmerOut2:input" />
  <s:link source="RNAmmerOut2:jobid" sink="out" />
  <s:link source="getSeq:parameters" sink="getSeqOut1:input" />
  <s:link source="getSeqIn1:output" sink="getSeq:parameters" />
  <s:link source="getSeqIn2:output" sink="getSeqIn1:parameters" />
  <s:link source="getSeqOut1:output" sink="getSeqOut2:input" />
  <s:link source="getSeqOut2:sequences" sink="RNAmmerIn2:sequences" />
  <s:source name="accession">
    <s:metadata>
      <s:description>Accession number for the organism, encapsulated with &lt;accession&gt;&lt;/accession&gt;</s:description>
    </s:metadata>
  </s:source>
  <s:sink name="out" />
</s:scufl>

