Ah ha - thanks. I was trying to click the link, but it kept crashing,
presumably because the files are too big. The URL method seems to work,
though.

I agree that it would be nice if there was a way to bump the files directly
into your history without the download/upload steps.

Thanks again for the help.
Jeremy

On Tue, Jul 19, 2011 at 1:20 PM, Jim Johnson <johns...@umn.edu> wrote:

>  Jeremy,
>
> Usually, the users saved the files to their local machine by clicking on
> the links, and then uploaded them again to the galaxy server.
> It can be possible to copy the link location, and paste it into the upload
> tools URL textarea.
>
> Ideally, it would be nice for the tool developer to be able to include a
> link in the html that would "promote" the file to a dataset in the current
> history.
>
> JJ
>
>
> On 7/19/11 3:08 PM, Jeremy Coate wrote:
>
> Thanks, Jim!
>
> I'll see if my limited Galaxy/bioinformatics skills can rise to the
> challenge of using your wrapper (I've never visited the "tool shed"
> before).
>
>  Out of curiosity, how did people use the files generated by the barcode
> splitter without this? I'm assuming there was/is a way, but I'm not figuring
> it out.
>
>  Jeremy
>
>
> On Tue, Jul 19, 2011 at 11:26 AM, Jim Johnson <johns...@umn.edu> wrote:
>
>>  I've had users make a similar request for the split files to appear in 
>> their history.
>> I made my own wrapper to enable this behavior.   It presents a list of 
>> barcodes from the barcode file input.  Any barcodes the user selects will 
>> have the resulting files copied to the users history as new datasets.
>>
>> I uploaded my barcode splitter tool configs to the toolshed:  
>> http://toolshed.g2.bx.psu.edu/  as repository: barcode_splitter
>>
>> JJ
>>
>>
>> Date: Mon, 18 Jul 2011 13:33:58 -0700
>> From: Jeremy Coate <je...@cornell.edu> <je...@cornell.edu>
>> To: David K Crossman <dkcro...@uab.edu> <dkcro...@uab.edu>
>> Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> 
>> <galaxy-user@lists.bx.psu.edu> <galaxy-user@lists.bx.psu.edu>
>> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter"
>> Message-ID:
>>      <caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com> 
>> <caa2bwd5ueraqeoueq97tfnhkwvhziq89whvr-oy04ov-k4j...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Thanks David,
>> I had considered this possibility but, curiously, the files don't show up in
>> the FastQ Groomer pull-down menu either. The original (multiplexed) data
>> file that I split using the Barcode Splitter is there (and, incidentally, I
>> ran FastQ Groomer on that before doing the barcode split), but none of the 3
>> files resulting from the splitter show up. Any other thoughts? It seems like
>> the new files just aren't landing in my history, though I can look at them
>> by clicking their links from the Barcode Splitter output.
>> Jeremy
>>
>> On Mon, Jul 18, 2011 at 12:01 PM, David K Crossman <dkcro...@uab.edu> 
>> <dkcro...@uab.edu> wrote:
>>
>>
>>  Jeremy,****
>>
>> ** **
>>
>>                 The files need to be groomed using the FastQ Groomer so
>> that they will end up in the fastqsanger state.  Then your files will show
>> up in the pull-down menus.****
>>
>> ** **
>>
>> David****
>>
>> ** **
>>
>> ** **
>>
>> *From:* galaxy-user-boun...@lists.bx.psu.edu 
>> [mailto:galaxy-user-boun...@lists.bx.psu.edu] *On Behalf Of *Jeremy Coate
>> *Sent:* Monday, July 18, 2011 1:44 PM
>> *To:* galaxy-user@lists.bx.psu.edu
>>
>> *Subject:* [galaxy-user] using files produced by "Barcode Splitter"****
>>
>> ** **
>>
>> I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries
>> into separate files. I would now like to map the reads from each of these
>> fastq files to a reference genome. However, the fastq files generated by
>> Barcode Splitter don't appear in the "Fastq File" pull-down menus within the
>> the BWA or Bowtie launch pages. I'm probably missing something obvious, but
>> what is the trick for making these files available for the mapping tools? Do
>> I need to import them into my history somehow?****
>>
>> ** **
>>
>> Thanks!
>> Jeremy****
>>
>>
>>
>>
>>
>>
>> ___________________________________________________________
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>
>
>
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