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Scful Workflow Example

<?xml version="1.0" encoding="UTF-8"?>
  <s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.1">
  <!-- Get EMBL accession number for Affymetrix probe set Id --> 
  <s:source>probeSetId</s:source>
  <s:link>
    <s:output>probeSetId</s:output>
    <s:input>AffyMapper_emblAccNumber:probeSetId</s:input>
  </s:link>
  <s:processor name="AffyMapper_emblAccNumber">  
    <s:arbitrarywsdl>  
      <s:wsdl>http://mygrid.ncl.ac.uk/axis/services/affymapper?wsdl</s:wsdl>
      <s:porttype>AffymetrixMapper</s:porttype>
      <s:operation>getAccessionNumber</s:operation>
    </s:arbitrarywsdl>   
  </s:processor>
  <s:link>
    <s:input>SrsEbiQuery_HgvbaseId:emblAccNumber</s:input>
    <s:output>AffyMapper_emblAccNumber:getAccessionNumberReturn</s:output>
  </s:link>
  <!-- Get HGVBASE Id for EMBL Accession Number -->
  <s:processor name="SrsEbiQuery_HgvbaseId">  
    <s:arbitrarywsdl>  
      <s:wsdl>http://mygrid.ncl.ac.uk/axis/services/SrsEbiQuery?wsdl</s:wsdl>  
      <s:porttype>SrsEbiQuery</s:porttype>  
      <s:operation>queryHgvbaseByEmblAccNumber</s:operation>  
    </s:arbitrarywsdl>  
  </s:processor>  
  <s:link>
    <s:input>SrsEbiQuery_HgvbaseEntries:usas</s:input>
    <s:output>SrsEbiQuery_HgvbaseId:queryHgvbaseByEmblAccNumberReturn</s:output>
  </s:link>
  <!-- Retrieve HGVBASE entries associated with Hgvbase Ids-->
  <s:processor name="SrsEbiQuery_HgvbaseEntries"> 
    <s:arbitrarywsdl>  
      <s:wsdl>http://mygrid.ncl.ac.uk/axis/services/SrsEbiQuery?wsdl</s:wsdl> 
      <s:porttype>SrsEbiQuery</s:porttype>  
      <s:operation>queryByArrayIds</s:operation>  
    </s:arbitrarywsdl> 
  </s:processor>
  <!-- Get Embl entry for Embl accession number -->
  <s:link>
    <s:input>SrsEbiQuery_emblEntry:usa</s:input>
    <s:output>AffyMapper_emblAccNumber:getAccessionNumberReturn</s:output>
  </s:link>
  <s:processor name="SrsEbiQuery_emblEntry">  
    <s:arbitrarywsdl>  
      <s:wsdl>http://mygrid.ncl.ac.uk/axis/services/SrsEbiQuery?wsdl</s:wsdl>  
      <s:porttype>SrsEbiQuery</s:porttype>  
      <s:operation>queryById</s:operation>  
    </s:arbitrarywsdl>  
  </s:processor>
  <!-- Merge SNP data with EMBL entry -->
  <s:link>
    <s:input>EmblSnpEdit_emblEntryWithSNPs:emblEntry</s:input>
    <s:output>SrsEbiQuery_emblEntry:queryByIdReturn</s:output>
  </s:link>
  <s:link>
    <s:input>EmblSnpEdit_emblEntryWithSNPs:hgvbaseEntries</s:input>
    <s:output>SrsEbiQuery_HgvbaseEntries:queryByArrayIdsReturn</s:output>
  </s:link>
  <s:processor name="EmblSnpEdit_emblEntryWithSNPs">  
    <s:arbitrarywsdl>  
      <s:wsdl>http://mygrid.ncl.ac.uk/axis/services/EmblSnpEdit?wsdl</s:wsdl>  
      <s:porttype>SnpFeatureEmblEditor</s:porttype>  
      <s:operation>mergeSnpData</s:operation>  
   </s:arbitrarywsdl>  
  </s:processor>  
  <s:sink>outfile_emblEntryWithSNPs</s:sink>
  <s:link>
    <s:input>outfile_emblEntryWithSNPs</s:input>
    <s:output>EmblSnpEdit_emblEntryWithSNPs:mergeSnpDataReturn</s:output>
  </s:link>
</s:scufl>

-- SylviaWong - 02 Dec 2004
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