<?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:4b0484a7-b6e2-446e-948a-a50106981b03" author="" title="hackworkfow" />
  <s:processor name="SwissprotPipe" boring="true">
    <s:stringconstant>whatizitSwissprot</s:stringconstant>
  </s:processor>
  <s:processor name="taggerParamXML">
    <s:defaults>
      <s:default name="text">lars dog1p p53_human knowledge</s:default>
      <s:default name="convertToHtml">false</s:default>
    </s:defaults>
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="contact" name="parameters" qname="{http://www.ebi.ac.uk/webservices/whatizit/ws}contact">
          <s:elements>
            <s:basetype optional="true" unbounded="false" typename="string" name="pipelineName" qname="contact&gt;pipelineName" />
            <s:basetype optional="true" unbounded="false" typename="string" name="text" qname="contact&gt;text" />
            <s:basetype optional="false" unbounded="false" typename="boolean" name="convertToHtml" qname="contact&gt;convertToHtml" />
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="omimQueryXmlParams">
    <s:defaults>
      <s:default name="databases_csv">omim</s:default>
      <s:default name="fields_csv">all</s:default>
      <s:default name="terms_csv">huntington</s:default>
      <s:default name="booleanOperator">AND</s:default>
    </s:defaults>
    <s:local>
      org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
      <s:extensions>
        <s:complextype optional="false" unbounded="false" typename="getMatchingEntries" name="parameters" qname="{http://www.embl.de/services/Retriever}getMatchingEntries">
          <s:elements>
            <s:basetype optional="false" unbounded="false" typename="string" name="databases_csv" qname="&gt;getMatchingEntries&gt;databases_csv" />
            <s:basetype optional="false" unbounded="false" typename="string" name="fields_csv" qname="&gt;getMatchingEntries&gt;fields_csv" />
            <s:basetype optional="false" unbounded="false" typename="string" name="terms_csv" qname="&gt;getMatchingEntries&gt;terms_csv" />
            <s:basetype optional="false" unbounded="false" typename="string" name="booleanOperator" qname="&gt;getMatchingEntries&gt;booleanOperator" />
          </s:elements>
        </s:complextype>
      </s:extensions>
    </s:local>
  </s:processor>
  <s:processor name="tag">
    <s:arbitrarywsdl>
      <s:wsdl>http://www.ebi.ac.uk/webservices/whatizit/ws?wsdl</s:wsdl>
      <s:operation>contact</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="queryOmim">
    <s:description>Queries the given "fields" in a user defined set of "databases" indexed 
                                by an SRS data integration system for the occurrence of the given "terms".
                                The fields must be exist in all of the databases being queried. Between 
                                fields and terms there is one-to-one correspondence. 
                                The field-term query pairs are combined by the "booleanOperator".
                                Allowed operator values are "AND", "OR" "BUTNOT"
                                Wild characters are allowed.
                                eg: retriever.getEntryIds("uniprot", "id,all", "PAX6_*|PAX7_*,fragment", "BUTNOT")));
                                this query searches uniprot for all the PAX6 or PAX7 protein sequences which are not fragments</s:description>
    <s:arbitrarywsdl>
      <s:wsdl>http://srs.embl.de/easy/Retriever?wsdl</s:wsdl>
      <s:operation>getMatchingEntries</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:link source="SwissprotPipe:value" sink="taggerParamXML:pipelineName" />
  <s:link source="omimQueryXmlParams:output" sink="queryOmim:parameters" />
  <s:link source="taggerParamXML:output" sink="tag:parameters" />
  <s:link source="queryOmim:parameters" sink="omimRecordsIds" />
  <s:link source="tag:parameters" sink="taggerOutput" />
  <s:sink name="taggerOutput" />
  <s:sink name="omimRecordsIds">
    <s:metadata>
      <s:mimeTypes>
        <s:mimeType>text/plain</s:mimeType>
      </s:mimeTypes>
    </s:metadata>
  </s:sink>
</s:scufl>

