<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" version="0.1" log="3">
  <s:processor name="os_format">
    <s:description>Type of format to be outputed by seqret</s:description>
    <s:stringconstant>fasta</s:stringconstant>
  </s:processor>
  <s:processor name="emblAccNumber">
    <s:stringconstant>embl:X07024</s:stringconstant>
  </s:processor>
  <s:processor name="trim_from">
    <s:stringconstant>1</s:stringconstant>
  </s:processor>
  <s:processor name="blast_database">
    <s:description>N.B. This must be a database ID recognised by the relevant blast.
pdb is ok
PDB just gives an error on invoking soaplab</s:description>
    <s:stringconstant>embl</s:stringconstant>
  </s:processor>
  <s:processor name="seqret">
    <s:description>Reads and writes (returns) sequences</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/edit::seqret</s:soaplabwsdl>
  </s:processor>
  <s:processor name="blastn_ncbi">
    <s:soaplabwsdl>http://www.ebi.ac.uk/collab/mygrid/service4/soap/services/alignment::blastn_ncbi</s:soaplabwsdl>
  </s:processor>
  <s:link>
    <s:input>seqret:osformat</s:input>
    <s:output>os_format:value</s:output>
  </s:link>
  <s:link>
    <s:input>emblRecord</s:input>
    <s:output>seqret:outseq</s:output>
  </s:link>
  <s:link>
    <s:input>seqret:sequence_usa</s:input>
    <s:output>emblAccNumber:value</s:output>
  </s:link>
  <s:link>
    <s:input>seqret:sbegin</s:input>
    <s:output>trim_from:value</s:output>
  </s:link>
  <s:link>
    <s:input>blastn_ncbi:query_sequence</s:input>
    <s:output>seqret:outseq</s:output>
  </s:link>
  <s:link>
    <s:input>blast_result</s:input>
    <s:output>blastn_ncbi:search_result</s:output>
  </s:link>
  <s:link>
    <s:input>blast_result_url</s:input>
    <s:output>blastn_ncbi:search_result_url</s:output>
  </s:link>
  <s:link>
    <s:input>blastn_ncbi:database</s:input>
    <s:output>blast_database:value</s:output>
  </s:link>
  <s:sink>
    emblRecord
    <s:metadata>
      <s:mimeTypes />
      <s:description>An EMBL record</s:description>
      <s:semanticType>http://www.mygrid.org.uk/ontology#EMBL_record</s:semanticType>
    </s:metadata>
  </s:sink>
  <s:sink>
    blast_result
    <s:metadata>
      <s:mimeTypes />
      <s:description />
      <s:semanticType />
    </s:metadata>
  </s:sink>
  <s:sink>
    blast_result_url
    <s:metadata>
      <s:mimeTypes />
      <s:description />
      <s:semanticType />
    </s:metadata>
  </s:sink>
</s:scufl>


