Hi,
>do you eventually know tha params for the blastprod processor at http://prodom.prabi.fr/prodom/current/wsdl/blastprodom.wsdl ? I don't think this service is still running. I never got it to work. Alternatively, you might be interested in using the following one which seems to be ok (see attached workflow): http://prodom.prabi.fr/prodom/current/wsdl/blastliteral.wsdl << Service Description: Operation: Executes blast on a blast (blastn or blastp) on ProDom Inputs: 1-query: a biological sequence (nucleotides or proteins, raw or fasta format) 2-program: select "blastp" for a blast against a protein database or "blastn" for a blast against a nucleotide database. 3-param: optional, parameter for your blast execution. The default is -j 10 -e 0.01 -h 0.001 >> Cheers, Franck _____ From: Achille Zappa [mailto:[email protected]] Sent: 27 March 2009 10:45 To: [email protected] Subject: [Taverna-users] BlastProDom- errata corrige Hi All sorry probably this is a copy of a previous mail but i made a mistake with e-mail address! but: I was looking around for a Protein Domains Analysis tool and i found that it should be exist a web service from ProDom and two related taverna workflows named prot_analysis.xml and workflow-nointerpro.xml but I am not able to find and download the files. do you know if they are still alive? Where i can find such scufl files? Or where i can find similar workflow? or do you eventually know tha params for the blastprod processor at http://prodom.prabi.fr/prodom/current/wsdl/blastprodom.wsdl ? thanks a lot regards
<?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:c6234332-c2d2-4b0f-9d22-afb495a8d9c6" author="" title="blastprodom" /> <s:processor name="blastprod1"> <s:description>blastprod alignment: alignment of the family, query: closest sequence to the consensus of the family (got by fetch_blast if needed), bank:data to blast against as fasta format, param: see blastprod help if 'default' will set -j 10 -e 0.01 -h 0.001 Takes an alignment, a bank and a query as input. Returns the standard blast ouput in xml without the 2 first none xml standards lines.</s:description> <s:arbitrarywsdl> <s:wsdl>http://prodom.prabi.fr/prodom/current/wsdl/blastliteral.wsdl</s:wsdl> <s:operation>blastprod</s:operation> </s:arbitrarywsdl> </s:processor> <s:processor name="outputWrapperXML"> <s:local> org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter <s:extensions> <s:complextype optional="false" unbounded="false" typename="blastprodResponse" name="outputWrapper" qname="{http://prodom.prabi.fr/blastprodom}blastprodResponse";> <s:elements> <s:basetype optional="false" unbounded="false" typename="string" name="blastprodOut" qname="{http://prodom.prabi.fr/blastprodom}>blastprodResponse>blastprodOut"; /> <s:basetype optional="false" unbounded="false" typename="string" name="blastprodImage" qname="{http://prodom.prabi.fr/blastprodom}>blastprodResponse>blastprodImage"; /> </s:elements> </s:complextype> </s:extensions> </s:local> </s:processor> <s:processor name="inputWrapperXML"> <s:local> org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter <s:extensions> <s:complextype optional="false" unbounded="false" typename="blastprod" name="inputWrapper" qname="{http://prodom.prabi.fr/blastprodom}blastprod";> <s:elements> <s:basetype optional="false" unbounded="false" typename="string" name="program" qname="{http://prodom.prabi.fr/blastprodom}>blastprod>program"; /> <s:basetype optional="false" unbounded="false" typename="string" name="query" qname="{http://prodom.prabi.fr/blastprodom}>blastprod>query"; /> <s:basetype optional="false" unbounded="false" typename="string" name="param" qname="{http://prodom.prabi.fr/blastprodom}>blastprod>param"; /> </s:elements> </s:complextype> </s:extensions> </s:local> </s:processor> <s:processor name="program" boring="true"> <s:stringconstant>blastp</s:stringconstant> </s:processor> <s:processor name="query" boring="true"> <s:stringconstant>KENGKFKVINKEMLSSGKINAIEGEIMHTDVKEPAKLGVRFNWFMPSAPYWV ISTDYENYSLVYSCTNILWLFHFDYA</s:stringconstant> </s:processor> <s:link source="blastprod1:outputWrapper" sink="outputWrapperXML:input" /> <s:link source="inputWrapperXML:output" sink="blastprod1:inputWrapper" /> <s:link source="program:value" sink="inputWrapperXML:program" /> <s:link source="query:value" sink="inputWrapperXML:query" /> <s:link source="outputWrapperXML:blastprodImage" sink="image" /> <s:link source="outputWrapperXML:blastprodOut" sink="blastReport" /> <s:sink name="blastReport" /> <s:sink name="image" /> </s:scufl>
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