Hello,
I think there are two problems:
1) When I run the workflow with that id "1J47", I get an empty list from
hsapiens_gene_ensembl. You have to configure the biomart to take a
PDB ID if you want to give it 1J47
2) The write_text_file takes a single string as its contents, so if you
were feeding a list of strings into it, it would be called once for each
string. As a result you would only get the last string in the list (the
others would be over written). Since there are no elements in the list,
the service is never being called and nothing is written to the file.
If you want to combine the output from the hsapiens_gene_ensembl into a
single string then you probably want to feed the list into
merge_string_list_to_string.
I think the attached workflow works.
Alan
<?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:net.sf.taverna:wfDefinition:6569c373-43cf-4539-b24f-88a4fdc7a5b3" author="" title="writingtextfile" />
<s:processor name="Write_Text_File">
<s:local>net.sourceforge.taverna.scuflworkers.io.TextFileWriter</s:local>
</s:processor>
<s:processor name="hsapiens_gene_ensembl">
<s:description>Homo sapiens genes (GRCh37)</s:description>
<s:biomart>
<biomart:MartQuery xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha";>
<biomart:MartService location="http://www.biomart.org/biomart/martservice"; />
<biomart:MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2010-03-08 14:50:08">
<biomart:MartURLLocation database="ensembl_mart_57" default="1" displayName="ENSEMBL GENES 57 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" />
</biomart:MartDataset>
<biomart:Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna">
<biomart:Dataset name="hsapiens_gene_ensembl">
<biomart:Attribute name="entrezgene" />
<biomart:Filter name="pdb" value="" list="true" />
</biomart:Dataset>
</biomart:Query>
</biomart:MartQuery>
</s:biomart>
</s:processor>
<s:processor name="Merge_string_list_to_string">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringListMerge</s:local>
</s:processor>
<s:link source="emblid" sink="hsapiens_gene_ensembl:hsapiens_gene_ensembl.pdb_filter" />
<s:link source="file" sink="Write_Text_File:outputFile" />
<s:link source="Merge_string_list_to_string:concatenated" sink="Write_Text_File:filecontents" />
<s:link source="hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene" sink="Merge_string_list_to_string:stringlist" />
<s:link source="Write_Text_File:outputFile" sink="out" />
<s:link source="hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene" sink="out2" />
<s:source name="file" />
<s:source name="emblid" />
<s:sink name="out" />
<s:sink name="out2" />
</s:scufl>
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
