Hi Jennifer, That's true. Completely forgot about this option which it is more convenient than downloading and re-importing. I still think I need the Multiple Output Files route cause I really want to automate the full processing of the data using the API. Thanks for pointing it out, Carlos On Tue, Sep 10, 2013 at 3:59 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Carlos,
Nice this is being worked on.
Just wanted to mention a quick tip for loading barcode splitter output: 1- right click on the output name & copy the link 2- open 'Get Data -> Upload File' tool, and paste link into box. Execute. 3- Repeat for all.
Data will load as dataset, no downloading/uploading required. I find that pasting all the links into a temp text file, then copy/paste all at once into the Upload tool speeds this up - as it then loads all in one go.
Not perfect, but maybe helpful for now.
Best, Jen Galaxy team
On Sep 10, 2013, at 11:49 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
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_o...
Best, Carlos
On Fri, Sep 6, 2013 at 1:58 PM, Carlos Borroto <carlos.borroto@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
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