HI Stian Thank you all for all the help.I was able to correct my
workflow .As some research group here has been using Taverna 1 instance and so
i am creating few workflows for them.And researchers over here would also like
to thank the Taverna team and the users forum for such a great tool and all the
help that we get from the user forum.Currently we are in the process of moving
to Taverna2 and for it we are also waiting on Taverna server compatible with
Taverna2 .We will mostly be using the Grid services from caBIG and also R for
this instance .Best RegardsRinkuOn Tue, 06 Apr 2010 16:17:18 +0530 wrote>On
Mon, Apr 5, 2010 at 21:39, Rinku Saha <[email protected]>
wrote:>> � I am trying to create a workflow where i am trying to write
the output into a txt file.Its not giving any error.But i am unable to find�
the� txt file in the location i gave (as file:///C:/jiangtaverna). Ineeded some
suggestions on where i am doing something wrong.Also wanted to ask how am i
going to name the output file.>> My inputs were:>> �
file:file:///C:/jiangtaverna>> � PDBid:1J47>>You've run into a few
issues here, I'm afraid..>>* The Write_Text_File local worker takes a
filename as an argument, not a URI.>* "file:" is included twice in your URI,
so it was not a valid URI>* You would not normally be allowed to write to
C:\ unless you are a>system administrator>* The Write_text_file takes a
single value as an input, but you want>to write the full list of items to
the file>* The BioMart query hsapiens_gene_ensembl returns 0 entries>*
You have configured the Biomart to filter by EMBL ID instead of Pubmed ID>*
BioMart expects the Pubmed ID witout the "PDBid:" prefix.>>>Try
instead:>>C:\Users\rinku\Desktop\jiangtaverna.txt as the file parameter
(Adjust>for path to your Desktop)>>You can inspect the intermediate
values from hsapiens_gene_ensembl, in>Taverna 1 select the processor in the
Status list, and then inspect>Intermediate Outputs. In Taverna 2.1.2,
double-click the service in>the diagram, and a pop-up should show the
intermediate outputs.>Alternatively you can also connect the output port of
the service to a>second workflow output port to inspect the values
returned.>>To avoid Taverna overwriting the same file for each value
returned>(Taverna does an iteration in cases of list cardinality
mismatches),>you will need to join the output list to a single string. One
way to>do this is to use the Local Worker "Merge string list to string".
If>you don't connect anything to "seperator" (sic) it will add line
feeds>between each string in the input. In your case I believe you
would>only get a single result back from BioMart, so this is less of
an>issue for you unless you feed a list of IDs to the 'emblid'
input.>>To change your workflow to accept pubmed IDs, configure the
Biomart>query for hsapiens_gene_emsembl and set the Filter to have a Gene
ID>list selected from "PDB IDs". You can either hardcode the IDs in
that>box, or override this by connecting to the filter input poer.
(like>you've done). BioMart has a web version called 'MartView' [2]
which>you might find useful to experiment with to get a feel about
different>filters and columns that can be retrieved.>>>See the
attached workflow were I've added these changes, running with:>>file:
C:\Users\stain\Desktop\ids.txt>pdbid: 1J47>>you will get the output
6736 stored to ids.txt.>>>(Note that the line feed inserted by Merge
is \n, not \r\n as is>common on Windows. You might want to inspect the
output file with a>text editor other than Notepad)>>>>Is there
any particular reason why you are using Taverna 1? For most>users we
recommend to try Taverna 2.1 [1] as it has many improvements>to the user
interface and workflow engine. We are however also very>interested in
feedback on reasons users are not transitioning to>Taverna
2.>>>>[1] http://www.taverna.org.uk/download/taverna-2-1/>[2]
http://www.biomart.org/biomart/martview/>>-->Stian Soiland-Reyes,
myGrid team>School of Computer Science>The University of
Manchester>------------------------------------------------------------------------------>Download
Intel® Parallel Studio Eval>Try the new software tools for yourself. Speed
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