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.

Timothy