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
<[email protected]> To: David K Crossman <[email protected]> Cc: "[email protected]"
<[email protected]> 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
<[email protected]> 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:*[email protected] [mailto:
[email protected]] *On Behalf Of *Jeremy Coate
*Sent:* Monday, July 18, 2011 1:44 PM
*To:*[email protected]
*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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