On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu <2hug...@gmail.com> wrote:

> On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
>
>> On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2hug...@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
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