<?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:P308SQKWX847" author="" title="" />
  <s:processor name="fieldName" boring="true">
    <s:stringconstant>Alltext</s:stringconstant>
  </s:processor>
  <s:processor name="Swissprot_Id" boring="true">
    <s:stringconstant>Q8BTW2</s:stringconstant>
  </s:processor>
  <s:processor name="parse_embl_id">
    <s:beanshell>
      <s:scriptvalue>String[] split = input.split("\n");
Vector nonEmpty = new Vector();

for (int i = 0; i &lt; split.length; i++) 
{		
	String trimmed = split[i].trim();
	String[] trimmedSplit = trimmed.split("=");
//	System.out.println(trimmedSplit.length);
	if (trimmedSplit.length &gt;= 2)
	{
	    if(trimmedSplit[0].equals("EMBL"))
	    {
		System.out.println(trimmedSplit[1]+"\n");
		nonEmpty.add(trimmedSplit[1].trim());
	    }
	    else
	    {
		System.out.println(trimmedSplit[0]+"\n");
	 	continue;
	    }	    	
	}
}

String output = "";

for (int i = 0; i &lt; nonEmpty.size(); i++)
{
	output = output + (String) (nonEmpty.elementAt(i) + "\n");
}</s:scriptvalue>
      <s:beanshellinputlist>
        <s:beanshellinput s:syntactictype="'text/plain'">input</s:beanshellinput>
      </s:beanshellinputlist>
      <s:beanshelloutputlist>
        <s:beanshelloutput s:syntactictype="'text/plain'">output</s:beanshelloutput>
      </s:beanshelloutputlist>
    </s:beanshell>
  </s:processor>
  <s:processor name="Uniprot_search">
    <s:description>To be added</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:1977/axis/services/uniprotsequence.uniprot</s:soaplabwsdl>
  </s:processor>
  <s:processor name="parse_uniprot">
    <s:description>Extract information from a Uniprot text file including PubMed, InterPro, Pfam and other related accession numbers</s:description>
    <s:soaplabwsdl>http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_uniprot</s:soaplabwsdl>
  </s:processor>
  <s:link source="Swissprot_Id:value" sink="Uniprot_search:searchterm" />
  <s:link source="Uniprot_search:result" sink="parse_uniprot:file_direct_data" />
  <s:link source="fieldName:value" sink="Uniprot_search:fieldname" />
  <s:link source="Uniprot_search:result" sink="uniprot_record" />
  <s:link source="parse_embl_id:output" sink="gene_description" />
  <s:link source="parse_uniprot:output" sink="parse_embl_id:input" />
  <s:link source="parse_uniprot:output" sink="parsed_data" />
  <s:sink name="uniprot_record" />
  <s:sink name="parsed_data" />
  <s:sink name="gene_description" />
</s:scufl>


