Re: [galaxy-user] using files produced by "Barcode Splitter"

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 <johns198@umn.edu mailto:johns198@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 <jec73@cornell.edu> <mailto:jec73@cornell.edu> To: David K Crossman <dkcrossm@uab.edu> <mailto:dkcrossm@uab.edu> Cc: "galaxy-user@lists.bx.psu.edu" <mailto:galaxy-user@lists.bx.psu.edu> <galaxy-user@lists.bx.psu.edu> <mailto:galaxy-user@lists.bx.psu.edu> Subject: Re: [galaxy-user] using files produced by "Barcode Splitter" Message-ID: <CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q@mail.gmail.com> <mailto:CAA2BWd5uERaqEoUeQ97TfNhkwvHziq89wHVR-Oy04ov-K4ju6Q@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 <dkcrossm@uab.edu> <mailto:dkcrossm@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-bounces@lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu> [mailto: galaxy-user-bounces@lists.bx.psu.edu <mailto:galaxy-user-bounces@lists.bx.psu.edu>] *On Behalf Of *Jeremy Coate *Sent:* Monday, July 18, 2011 1:44 PM *To:* galaxy-user@lists.bx.psu.edu <mailto: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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