The "fromFastaToGenericSequence" requires some kind of XML input just like
ClustalW. I have no idea how to construct that xml.
I am extracting sequence from following xml (that I get from ncbi entrez
utility) and this service https://www.biocatalogue.org/services/2182 (
http://www.myexperiment.org/workflows/1705.html) is not accepting it.
<TSeq>
<TSeq_seqtype value="nucleotide"/>
<TSeq_gi>636528437</TSeq_gi>
<TSeq_accver>KJ543728.1</TSeq_accver>
<TSeq_taxid>333760</TSeq_taxid>
<TSeq_orgname>Human papillomavirus type 16</TSeq_orgname>
<TSeq_defline>Human papillomavirus type 16 isolate 50031 protein E6 (E6)
gene, complete cds</TSeq_defline>
<TSeq_length>772</TSeq_length>
<TSeq_sequence>GCTTGTTTTAACT....ACCTAC</TSeq_sequence>
</TSeq>
The given example sequence is following
>seq1MMGSVELNLRETELCLGLPGGD>seq2MMGSVELNLRETEICLGLPEGD>seq3MMGLVELNLRETEICLGLPEGD
But it gives following error on both example sequence and if I replace the
sequence with my values
Processor 'run' - Port 'parameters': An error occurred invoking the WSDL
service
Invalid parameters:
Sequence -> Error in reading input sequence. Please check your input.
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
org.apache.xerces.parsers.AbstractSAXParser.endElement(unknown file)
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(unknown file)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(unknown
file)
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(unknown
file)
org.apache.xerces.parsers.XML11Configuration.parse(unknown file)
org.apache.xerces.parsers.XML11Configuration.parse(unknown file)
org.apache.xerces.parsers.XMLParser.parse(unknown file)
org.apache.xerces.parsers.AbstractSAXParser.parse(unknown file)
org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(unknown file)
org.apache.xerces.jaxp.SAXParserImpl.parse(unknown file)
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
org.apache.axis.client.Call.invokeEngine(Call.java:2784)
org.apache.axis.client.Call.invoke(Call.java:2767)
org.apache.axis.client.Call.invoke(Call.java:1910)
net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invokeCall(WSDLSOAPInvoker.java:198)
net.sf.taverna.wsdl.soap.WSDLSOAPInvoker.invoke(WSDLSOAPInvoker.java:139)
net.sf.taverna.t2.activities.wsdl.T2WSDLSOAPInvoker.invoke(T2WSDLSOAPInvoker.java:281)
net.sf.taverna.t2.activities.wsdl.WSDLActivity$1.run(WSDLActivity.java:289)
java.lang.Thread.run(Thread.java:724)
On Tue, Jun 17, 2014 at 3:38 PM, Stian Soiland-Reyes <
[email protected]> wrote:
> For the BioMoby clustalW services, I believe you need to construct a
> 'Sequence' object, but I am afraid I am not sure how to do that ("Add
> Parser" only suggests output parsers for those). My best guess would
> be using the "fromFastaToGenericSequence" service in front of the
> input to BioMoby ClustalW.
>
>
> Alternatively, did you try any of these web services?
>
> https://www.biocatalogue.org/search?utf8=%E2%9C%93&q=CLUSTALW&commit=
>
> Perhaps
> https://www.biocatalogue.org/services/2182
> is a good try - see documentation at:
> http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap
>
>
> That documentation recommends Clustal Omega instead, which I have not
> tried:
>
> http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalo_soap
>
>
>
> On 17 June 2014 09:55, Muhammad Usama <[email protected]> wrote:
> > I have made a workflow which returns the FASTA of search results from
> ncbi
> > as a list. There is a Moby component for CLUSTALW but it is not accepting
> > list format or comma separated FASTA.
> >
> > Which component I can use to run CLUSTALW on the list that I have?
> >
> > --
> > Muhammad Usama
> >
> >
> ------------------------------------------------------------------------------
> > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> > Find What Matters Most in Your Big Data with HPCC Systems
> > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> > Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> > http://p.sf.net/sfu/hpccsystems
> > _______________________________________________
> > taverna-users mailing list
> > [email protected]
> > [email protected]
> > Web site: http://www.taverna.org.uk
> > Mailing lists: http://www.taverna.org.uk/about/contact-us/
> >
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
> http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> taverna-users mailing list
> [email protected]
> [email protected]
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/about/contact-us/
>
--
Muhammad Usama
2011-NUST-MS-CS-009
------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
_______________________________________________
taverna-users mailing list
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Mailing lists: http://www.taverna.org.uk/about/contact-us/
