Timothy Wu wrote:
On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu <2huggie@gmail.com> wrote:
On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2huggie@gmail.com> wrote:
I think I need some kind of "data source" implementation that allow user
to
obtain the data themselves. However with the current tool XML definition, I don't know how to have a FTP download tool to download EST data from NCBI to Galaxy directly.
Perhaps I have misunderstood you, but I'd just use the provided "Upload Data" tool, and paste in the FTP URL for the file, e.g. an NCBI FTP URL.
I wasn't aware that the Upload data tool could take a FTP URL, so thanks for letting me know.
Unfortunately that doesn't take a wild card.
I need to have the path specification like this " ftp://ftp.ncbi.nih.gov/genbank/gbest*.seq.gz" at the minimum.
Actually my tool is more versatile (though I don't need it for this particular application).
I could specify
ftp://ftp.ncbi.nih.gov/genomes/*/*/NC_*.fna
and grab all the fasta files for all chromosome of all species under the genomes directory. I thought it would be a nice tool to have in my galaxy arsenal.
It looks to me like a good idea to check out how the upload tool is implemented. But it seems a bit complex. I don't understand why it does not have the <outputs> tag, it also has this action tab <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> which is not explained in the "Tool Config Syntax".
Any documentations or tutorials out there that would help me understand how to implement this?
Timothy
Hi Timothy, The default action taken when executing a tool is to call the execute() method in lib/galaxy/tools/actions/__init__.py in DefaultToolAction. This method prepares the tool and creates a job to run the tool. The upload tool is unlike other tools and can't use this default method, so it instead uses an action in upload.py in the same directory. This would probably be easiest as a new tool, however, since it's a very specialized case. --nate
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