Hi Graham,

There was an issue with the dataset collection code that was preventing this 
sample wrapper from working.  This has been fixed in 6426:187267753315, and the 
wrapper now functions properly for me, displaying all 5 files.  Let me know if 
this works for you after you've updated.

Thanks!

-Dannon


On Dec 6, 2011, at 7:02 AM, graham etherington (TSL) wrote:

> Hi,
> Thanks for the input.
> I've attached code (tool xml and perl script tool) and a test file for a
> simple example that creates variable amounts of files after tool
> execution. The test file is a simple 4 line text file for which new file
> is created for each line in it and then that line is written to the new
> file. An additional output file is also written with some runtime
> information in it.
> The files should run as-is, just edit your tool_conf.xml, upload Test.txt
> and it should work.
> This example creates the normal 'dataset_12345.dat' files and doesn't use
> a sub-directory (e.g. datset_12345_files). If someone can get that to
> work, that would be pretty good.
> All the best,
> Graham
> 
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
> 
> On 05/12/2011 13:37, "Dannon Baker" <dannonba...@me.com> wrote:
> 
>> Graham,
>> 
>> How are the output files being handled in
>> split_var_length_barcodes_wrapper.py?  See
>> http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a
>> reference-- you're going to want to follow the bottom example there
>> involving $__new_file_path__ and the naming convention specified.
>> 
>> On a side note, this is something I've brushed up against recently
>> myself, I'd be very interested in seeing what you come up with.
>> 
>> -Dannon
>> 
>> On Dec 5, 2011, at 6:47 AM, graham etherington (TSL) wrote:
>> 
>>> Hi,
>>> I'm developing a barcode splitter, which will split barcodes of variable
>>> length and then put them into the history for downstream analysis
>>> (currently FASTX barcode splitter only splits barcodes of the same
>>> length
>>> and the user has to download the data through an html link). The number
>>> of
>>> output files can't be determined until the tool has executed as it will
>>> depend on the number of barcodes presented.
>>> Here is an abridged version of the tool xml file:
>>> 
>>> <tool id="split_var_barcodes" name="Split barcodes of variable length"
>>> version="1.0.0" force_history_refresh="True">
>>>     <command interpreter="python">split_var_length_barcodes_wrapper.py
>>> $input
>>> $barcodes $output.extra_files_path  $output </command>
>>> <inputs>            <param format="txt" name="barcodes" type="data"
>>> label="Barcodes
>>> to use" />
>>>             <param format="fasta,fastqsanger,fastqsolexa,fastqillumina"
>>> name="input"
>>> type="data" label="Library to split" />
>>>     </inputs>
>>>     
>>>     <outputs>
>>>             <data format="html" name="output" />
>>>     </outputs>
>>> </tool>
>>> 
>>> When I run the tool, the $output file to which I write various tool
>>> progress stuff is written and is displayed in the history. Also, the
>>> spit
>>> barcode files are written to a sub-directory of the same name as the
>>> output file.
>>> In the Galaxy database, if the $output file is named dataset_11940.dat
>>> then an example barcode file name and path is:
>>> 
>>> /home/galaxy/software/galaxy-central/database/files/011/dataset_11940_fil
>>> es
>>> /AACAGAGT.fastq
>>> 
>>> Unfortunately, the split barcode files are not being displayed in the
>>> history, so I was wondering if anyone could see any problems in what I'm
>>> doing.
>>> 
>>> Many thanks,
>>> Graham
>>> 
>>> 
>>> 
>>> 
>>> Dr. Graham Etherington
>>> Bioinformatics Support Officer,
>>> The Sainsbury Laboratory,
>>> Norwich Research Park,
>>> Norwich NR4 7UH.
>>> UK
>>> Tel: +44 (0)1603 450601
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>> 
> 
> <multi.pl><multi.xml><Test.txt>

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