Cool, I got a tweet about this tool from @GalaxyProject[1]. 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"[2] 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. [1]https://twitter.com/galaxyproject/status/377497531745595392 [2]http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run Best, Carlos On Fri, Sep 6, 2013 at 1:58 PM, Carlos Borroto <carlos.borr...@gmail.com> wrote: > Hi, > > 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): > http://testtoolshed.g2.bx.psu.edu/view/cjav/split_by_barcode > > 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 > easy. > > I have to say big thanks to Biopython and this[1] anonymous soul for > making it quite easy to write the actual code doing the heavy lifting. > > [1]https://gist.github.com/dgrtwo/3725741 > > Cheers, > Carlos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
