Thank you very much, that worked as expected. I converted pubmed results
like
> 636528437
GCTTGTTTTAACT....ACCTAC
and ClustalW workflow worked perfectly on this.
Thank you :)
On Thu, Jun 19, 2014 at 3:01 PM, Stian Soiland-Reyes <
[email protected]> wrote:
> For the EBI services documentation is available both on their website,
> and within the XML splitters. Note that as EBI services are highly
> configurable you might sometimes need to add an input splitter to an
> input splitter parameter.
>
> http://www.myexperiment.org/workflows/1768 is a better example, it
> sees that the workflow 1705 had somehow lost all the newlines in the
> example input which made it no longer a valid FASTA sequence.
>
> Example input:
>
> >seq1
> MMGSVELNLRETELCLGLPGGD
>
> >seq2
> MMGSVELNLRETEICLGLPEGD
>
> >seq3
> MMGLVELNLRETEICLGLPEGD
>
>
> produces:
>
> CLUSTAL 2.1 multiple sequence alignment
>
>
> seq2 MMGSVELNLRETEICLGLPEGD
> seq3 MMGLVELNLRETEICLGLPEGD
> seq1 MMGSVELNLRETELCLGLPGGD
> *** *********:***** **
>
>
> (and many other formats)
>
>
> To generate such a FASTA input from your XML I would try to merge:
>
> <TSeq_gi>636528437</TSeq_gi>
> <TSeq_sequence>GCTTGTTTTAACT....ACCTAC</TSeq_sequence>
>
> to produce
>
> > 636528437
> GCTTGTTTTAACT....ACCTAC
>
>
> and then merge those again to a larger string.
>
>
> You can use a nested workflow with a couple of "Concatenate string".
> If you are unable to use an XML output splitter to extract TSeq_gi
> from upstream (you did not send your workflow and I don't know which
> service you used), then you can alternatively use two of the XPath
> services, which has a GUI where you can paste that XML and select the
> right element.
>
>
>
>
> On 18 June 2014 17:43, Muhammad Usama <[email protected]> wrote:
> > Only if I knew what kind of XML it is expecting. Many services and
> > components are missing documentations.
> >
> >
> > On Wed, Jun 18, 2014 at 8:50 PM, Stian Soiland-Reyes
> > <[email protected]> wrote:
> >>
> >> See http://dev.mygrid.org.uk/wiki/display/tav250/WSDL#WSDL-XMLSplitters
> >>
> >> for how to use XML Splitters to construct the XML the service expects
> >> (and to deconstruct what it returns).
> >>
> >> On 18 June 2014 14:09, Muhammad Usama <[email protected]>
> wrote:
> >> > 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
> >> > [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
> > [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
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