On Friday, September 23, 2011, Timothy Wu <2huggie@gmail.com> wrote:
> On Thu, Sep 22, 2011 at 4:36 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
>>
>> How does your tool handle this at the command line (ignoring Galaxy)?
>> Does it expect a directory name or pattern, or just a really long
>> command line string with many many file names?
>
> Originally I have this config text file which specify a directory. And scripts will look into this directory for specific file name patterns. Since galaxy specifies its own file names, the pattern would not work.
>
> I'm actually tailoring my tools for galaxy because my original design is not flexible and it's just not well thought out. With galaxy I'm pretty happy that I get to split my tools up to be more fine-grained to attempt to stick to the Unix tool's "Write programs that do one thing and do it well" philosophy (well, more to the "one" part than to the "well" part).
>
> I am thinking of a few work-arounds.
>

Do they need to be separate input files, or could they be concatenated?

For example, rather than feeding in 10 individual FASTA files (each with multiple sequences), could it take a single concatenated FASTA file? That may not make sense for your tool, but it seems a more elegant solution if it does.

Then the question becomes how best to prepare the big FASTA input within Galaxy ;-)

Peter