Cool, I got a tweet about this tool from @GalaxyProject.
To further explain what I'm trying to accomplish here, as I realized
not everybody might know what using "Multiple Output Files" and
specifically "Number of Output datasets cannot be determined until
tool run" entails.
The current Barcode Splitter available on Galaxy Main and based on
FASTX-toolkit by Assaf Gordon, makes all output files accessible
through HTML links. This is not very convenient, as if you want to
use, and you probably do, these outputs in a downstream analysis
inside Galaxy, your only solution right now is to download the linked
files in the HTML output and manually re-import then into Galaxy. The
tool I wrote includes the option of writing the output files(splitted
FASTA or FASTQ files) with a naming convention that can be used with
Galaxy's "Multiple Output Files" so all results files are
automatically added to your history. I believe you still can't easily
use this tool upstream in a workflow. As I far as I can tell tools
without a known number of outputs can't be used upstream in workflows.
I do think you can accomplish some automation using the API, although
I haven't tested this yet.
On Fri, Sep 6, 2013 at 1:58 PM, Carlos Borroto <carlos.borr...@gmail.com> wrote:
> I was wondering if I could get someone to test this new barcode
> splitter I wrote. The main reason for me to duplicate the already
> great fastx-toolkit based splitter, is so I can use galaxy's multiple
> output capabilities.
> You can find this tool in the testtoolshed for now(after some more
> testing I will moved to the main toolshed):
> Hopefully I got Galaxy's tool dependency system right(it works on my
> box, not that this says much) and installing this tool should be quite
> I have to say big thanks to Biopython and this anonymous soul for
> making it quite easy to write the actual code doing the heavy lifting.
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