<?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:www.mygrid.org.uk:operation:7N62B8VKYQ1" author="" title="" />
  <s:processor name="format">
    <s:stringconstant>-w</s:stringconstant>
  </s:processor>
  <s:processor name="FASTA">
    <s:stringconstant>-F</s:stringconstant>
  </s:processor>
  <s:processor name="Protein_type">
    <s:stringconstant>nonplant</s:stringconstant>
  </s:processor>
  <s:processor name="nr">
    <s:stringconstant>nr</s:stringconstant>
  </s:processor>
  <s:processor name="tblastn">
    <s:stringconstant>tblastn</s:stringconstant>
  </s:processor>
  <s:processor name="blastp">
    <s:stringconstant>blastp</s:stringconstant>
  </s:processor>
  <s:processor name="sumoplot">
    <s:description>wrapper to run SUMOplot</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::sumoplot</s:soaplabwsdl>
  </s:processor>
  <s:processor name="copyright">
    <s:description>script to generate copyright statement</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/documentation::copyright</s:soaplabwsdl>
  </s:processor>
  <s:processor name="signalp">
    <s:description>wrapper to run SignalP</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::signalp</s:soaplabwsdl>
  </s:processor>
  <s:processor name="blastwrapper2">
    <s:description>Wrapper for BLAST at NCBI</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::blastwrapper2</s:soaplabwsdl>
  </s:processor>
  <s:processor name="PSORTII">
    <s:description>Predicts peptide localisation signals</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::psortiiwrapper</s:soaplabwsdl>
  </s:processor>
  <s:processor name="iPSORT">
    <s:description>Predicts peptide localisation signals</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::ipsortwrapper</s:soaplabwsdl>
  </s:processor>
  <s:processor name="pscan">
    <s:description>Scans proteins using PRINTS</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_motifs::pscan</s:soaplabwsdl>
  </s:processor>
  <s:processor name="targetp">
    <s:description>wrapper to run TargetP</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::targetp</s:soaplabwsdl>
  </s:processor>
  <s:processor name="blastwrapper21">
    <s:description>Wrapper for BLAST at NCBI</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:8081/axis/services/seq_analysis::blastwrapper2</s:soaplabwsdl>
  </s:processor>
  <s:processor name="pepwindow">
    <s:description>Displays protein hydropathy</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_composition::pepwindow</s:soaplabwsdl>
  </s:processor>
  <s:processor name="pepcoil">
    <s:description>Predicts coiled coil regions</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_2d_structure::pepcoil</s:soaplabwsdl>
  </s:processor>
  <s:processor name="PepStats">
    <s:description>Protein statistics</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_composition::pepstats</s:soaplabwsdl>
  </s:processor>
  <s:processor name="epestfind">
    <s:description>Finds PEST motifs as potential proteolytic
                  cleavage sites</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_motifs::epestfind</s:soaplabwsdl>
  </s:processor>
  <s:processor name="HelixTurnHelix">
    <s:description>Report nucleic acid binding motifs</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/protein_2d_structure::helixturnhelix</s:soaplabwsdl>
  </s:processor>
  <s:processor name="proteinraw">
    <s:description>InterProScan with output in TXT format, for protein</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/interproscan::proteinraw</s:soaplabwsdl>
  </s:processor>
  <s:processor name="getorf">
    <s:description>Finds and extracts open reading frames
                  (ORFs)</s:description>
    <s:soaplabwsdl>http://industry.ebi.ac.uk/soap/soaplab/nucleic_gene_finding::getorf</s:soaplabwsdl>
  </s:processor>
  <s:processor name="ParseBLAST">
    <s:arbitrarywsdl>
      <s:wsdl>http://don.dcs.shef.ac.uk/mygrid/wsdl/a_ParseBLAST.wsdl</s:wsdl>
      <s:operation>ParseBLAST</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="GetMeSH">
    <s:arbitrarywsdl>
      <s:wsdl>http://don.dcs.shef.ac.uk/mygrid/wsdl/a_GetMeSH.wsdl</s:wsdl>
      <s:operation>GetMeSH</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="FilterMeSH">
    <s:arbitrarywsdl>
      <s:wsdl>http://don.dcs.shef.ac.uk/mygrid/wsdl/a_FilterMeSH.wsdl</s:wsdl>
      <s:operation>FilterMeSH</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:processor name="MeSHtoPMID">
    <s:arbitrarywsdl>
      <s:wsdl>http://don.dcs.shef.ac.uk/mygrid/wsdl/a_MeSHtoPMID.wsdl</s:wsdl>
      <s:operation>MeSHtoPMID</s:operation>
    </s:arbitrarywsdl>
  </s:processor>
  <s:link source="PROTEINFASTA" sink="PepStats:sequence_direct_data" />
  <s:link source="PROTEINFASTA" sink="PSORTII:proteinseq_direct_data" />
  <s:link source="PROTEINFASTA" sink="iPSORT:proteinseq_direct_data" />
  <s:link source="PROTEINFASTA" sink="HelixTurnHelix:sequence_direct_data" />
  <s:link source="FASTA:value" sink="iPSORT:fasta" />
  <s:link source="format:value" sink="PSORTII:format" />
  <s:link source="PepStats:outfile" sink="PepStats_Out" />
  <s:link source="PSORTII:output" sink="ProteinLocation" />
  <s:link source="HelixTurnHelix:outfile" sink="HTH_NucBindingSites" />
  <s:link source="iPSORT:output" sink="ProteinLocation_2" />
  <s:link source="Protein_type:value" sink="iPSORT:proteintype" />
  <s:link source="PROTEINFASTA" sink="signalp:seqfile_direct_data" />
  <s:link source="signalp:outfile_url" sink="SP_url" />
  <s:link source="signalp:outfile_seq" sink="SP_outseq" />
  <s:link source="PROTEINFASTA" sink="sumoplot:seqfile_direct_data" />
  <s:link source="sumoplot:output" sink="sumo_out" />
  <s:link source="copyright:out" sink="COPYRIGHT_INFO" />
  <s:link source="PROTEINFASTA" sink="blastwrapper2:query_file_direct_data" />
  <s:link source="blastp:value" sink="blastwrapper2:program" />
  <s:link source="nr:value" sink="blastwrapper2:database" />
  <s:link source="blastwrapper2:output" sink="Blastp_nr_out" />
  <s:link source="PROTEINFASTA" sink="blastwrapper21:query_file_direct_data" />
  <s:link source="nr:value" sink="blastwrapper21:database" />
  <s:link source="tblastn:value" sink="blastwrapper21:program" />
  <s:link source="blastwrapper21:output" sink="tblastn_nr_out" />
  <s:link source="PROTEINFASTA" sink="targetp:seqfile_direct_data" />
  <s:link source="targetp:outfile_url" sink="TargetP_out" />
  <s:link source="PROTEINFASTA" sink="pscan:sequence_direct_data" />
  <s:link source="pscan:outfile" sink="pscan_out" />
  <s:link source="PROTEINFASTA" sink="pepcoil:sequence_direct_data" />
  <s:link source="pepcoil:outfile" sink="pepcoil_out" />
  <s:link source="PROTEINFASTA" sink="epestfind:sequence_direct_data" />
  <s:link source="epestfind:outfile" sink="ePEST_out" />
  <s:link source="PROTEINFASTA" sink="proteinraw:sequence" />
  <s:link source="proteinraw:result" sink="InterproRaw_out" />
  <s:link source="epestfind:Graphics_in_PNG" sink="epest_GraphicsPNG" />
  <s:link source="PROTEINFASTA" sink="pepwindow:sequence_direct_data" />
  <s:link source="pepwindow:Graphics_in_PNG" sink="pepwindow_Graphics" />
  <s:link source="ParseBLAST:PMIDList" sink="GetMeSH:PMIDList" />
  <s:link source="GetMeSH:MeSHList" sink="FilterMeSH:MeSHListIn" />
  <s:link source="FilterMeSH:MeSHListOut" sink="MeSHtoPMID:MeSHLIST" />
  <s:link source="MeSHtoPMID:PMIDLIST" sink="PMIDList" />
  <s:link source="blastwrapper2:output" sink="ParseBLAST:BlastReport" />
  <s:source name="PROTEINFASTA" />
  <s:sink name="PepStats_Out" />
  <s:sink name="HTH_NucBindingSites" />
  <s:sink name="ProteinLocation" />
  <s:sink name="ProteinLocation_2" />
  <s:sink name="SP_url" />
  <s:sink name="SP_outseq" />
  <s:sink name="sumo_out" />
  <s:sink name="COPYRIGHT_INFO" />
  <s:sink name="Blastp_nr_out" />
  <s:sink name="tblastn_nr_out" />
  <s:sink name="TargetP_out" />
  <s:sink name="pscan_out" />
  <s:sink name="pepcoil_out" />
  <s:sink name="ePEST_out" />
  <s:sink name="InterproRaw_out" />
  <s:sink name="epest_GraphicsPNG">
    <s:metadata>
      <s:mimeTypes>
        <s:mimeType>application/octet-stream</s:mimeType>
        <s:mimeType>image/png</s:mimeType>
      </s:mimeTypes>
    </s:metadata>
  </s:sink>
  <s:sink name="pepwindow_Graphics">
    <s:metadata>
      <s:mimeTypes>
        <s:mimeType>application/octet-stream</s:mimeType>
        <s:mimeType>image/png</s:mimeType>
      </s:mimeTypes>
    </s:metadata>
  </s:sink>
  <s:sink name="PMIDList" />
</s:scufl>



