Hello all,
I've tried to use attached worklow (which gets fasta sequence from
Swissprot related to an accession number) with bootstrapper
(./executeworkflow.sh, which calls ./taverna-bootstrap-1.7.2.1.jar) but
instead of creating 2 result files ("fastaSequence" and "output"), it
has created 2 folders/directories with these names, but without any content.
Here is the command line I use :
../executeworkflow.sh -input SwissProtAcc
protic_accession_5004616955195094923.txt
file:getFastaSeqFromSwissProtAcc.xml -output ./result
Files are in attachment. For information:
$ ls -lFh result/
total 8,0K
drwxr-xr-x 2 rflores rflores 4,0K 2010-06-28 15:03 fastaSequence/
-rw-r--r-- 1 rflores rflores 2,3K 2010-06-28 15:03 progressReport.xml
$ java -version
java version "1.6.0_0"
OpenJDK Runtime Environment (build 1.6.0_0-b11)
OpenJDK Client VM (build 1.6.0_0-b11, mixed mode, sharing)I get this
behavour only with this workflow. Any idea why ? And how make the
workflow outputs being text files rather than folders ?
Any help would be greatly appreciated.
Raphaël.
<?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:d79e224e-0f88-44b9-bffc-3258d7085da3" author="" title="getFastaSeqFromSwissProt" />
<s:processor name="BIND_IdSearchGetFastaBySwissProtId">
<s:description>Searches over the BIND protein-protein interaction database for the specified id and returns hits as FASTA sequences</s:description>
<s:biomobywsdl>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>BIND_IdSearchGetFastaBySwissProtId</s:serviceName>
<s:authorityName>bioinfo.icapture.ubc.ca</s:authorityName>
</s:biomobywsdl>
</s:processor>
<s:processor name="Object">
<s:description>an object</s:description>
<s:biomobyobject>
<s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
<s:serviceName>Object</s:serviceName>
<s:authorityName />
</s:biomobyobject>
</s:processor>
<s:processor name="Parse_Moby_Data_FASTA">
<s:description>Processor to parse the datatype FASTA</s:description>
<s:biomobyparser>
<s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
<s:datatype>FASTA</s:datatype>
<s:articleName>hits</s:articleName>
<s:description>Processor to parse the datatype FASTA</s:description>
</s:biomobyparser>
</s:processor>
<s:processor name="namespace_value" boring="true">
<s:stringconstant>Swiss-Prot</s:stringconstant>
</s:processor>
<s:link source="BIND_IdSearchGetFastaBySwissProtId:FASTA(Collection - 'hits' As Simples)" sink="Parse_Moby_Data_FASTA:mobyData('FASTA')" />
<s:link source="Object:mobyData" sink="BIND_IdSearchGetFastaBySwissProtId:Object(id)" />
<s:link source="SwissProtAcc" sink="Object:id" />
<s:link source="namespace_value:value" sink="Object:namespace" />
<s:link source="BIND_IdSearchGetFastaBySwissProtId:output" sink="output" />
<s:link source="Parse_Moby_Data_FASTA:hits_'content'" sink="fastaSequence" />
<s:source name="SwissProtAcc" />
<s:sink name="fastaSequence" />
<s:sink name="output" />
</s:scufl>
Q43638
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