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> To: David K Crossman <dkcrossm@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-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> wrote:

Jeremy,****

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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.****

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David****

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*From:*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 *Subject:* [galaxy-user] using files produced by "Barcode Splitter"****

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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?****

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Thanks! Jeremy****