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