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,****

** **

                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] *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****