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> To: David K Crossman <dkcro...@uab.edu> Cc: "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> 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> 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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