Hi,
my Taverna1 workflow (attachment) does not open with Taverna2
"Could not parse Scufl file"
regards,
Silvia
<?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:3HN745VV5Z0" author="" title="" />
<s:processor name="affyclean">
<s:beanshell>
<s:scriptvalue>char space=' ';
int code=20; // this is the char code
// of the irritating ctrl char
char rubbish=(char) code;
String clean = CEL.replace(rubbish,space);</s:scriptvalue>
<s:beanshellinputlist>
<s:beanshellinput s:syntactictype="'text/plain'">CEL</s:beanshellinput>
</s:beanshellinputlist>
<s:beanshelloutputlist>
<s:beanshelloutput s:syntactictype="'text/plain'">clean</s:beanshelloutput>
</s:beanshelloutputlist>
</s:beanshell>
</s:processor>
<s:processor name="background" boring="true">
<s:stringconstant>mas</s:stringconstant>
</s:processor>
<s:processor name="normalize" boring="true">
<s:stringconstant>constant</s:stringconstant>
</s:processor>
<s:processor name="affyallocate">
<s:description>Allocates a space for affy-expresso analysis</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12851/axis/services/microarrays.affyallocate</s:soaplabwsdl>
</s:processor>
<s:processor name="filesuck">
<s:description>CEL file transfer</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12851/axis/services/microarrays.filesuck</s:soaplabwsdl>
</s:processor>
<s:processor name="affyexpresso">
<s:description>Bioconductor example using affy expresso (multiple CEL files via ref)</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12851/axis/services/microarrays.affyexpresso</s:soaplabwsdl>
</s:processor>
<s:processor name="Remove_duplicate_strings" boring="true">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates</s:local>
</s:processor>
<s:processor name="Merge_string_list_to_string" boring="true">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringListMerge</s:local>
</s:processor>
<s:link source="in1" sink="affyclean:CEL" />
<s:link source="Merge_string_list_to_string:concatenated" sink="affyexpresso:dir" />
<s:link source="Remove_duplicate_strings:strippedlist" sink="Merge_string_list_to_string:stringlist" />
<s:link source="Merge_string_list_to_string:concatenated" sink="out3" />
<s:link source="affyallocate:dir" sink="filesuck:indir" />
<s:link source="affyclean:clean" sink="filesuck:file1_direct_data" />
<s:link source="background:value" sink="affyexpresso:bgcorrect" />
<s:link source="filesuck:outdir" sink="Remove_duplicate_strings:stringlist" />
<s:link source="affyexpresso:result" sink="out" />
<s:link source="normalize:value" sink="affyexpresso:normalize" />
<s:source name="in1" />
<s:sink name="out" />
<s:sink name="out3" />
</s:scufl>
------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
taverna-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/taverna-users
Documentation: http://www.mygrid.org.uk/usermanual1.7/
FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq
Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
