On Wed, Sep 12, 2012 at 4:04 PM,  <kauerb...@comcast.net> wrote:
> Hello,
> I'm new to Galaxy and have a very basic question.  If I upload a dataset,
> (say, a protein sequence file in fasta format), and I want to use one of the
> tools on this dataset, what do I have to do to make the tool aware of my
> dataset?  When I tried it the tools did not know that my uploaded data file
> existed.
> Thank you.

You need to make sure your dataset is recognised as 'fasta',
which can be checked/edited via the 'pencil' icon.

As long as the tool's XML file defines the input as type 'fasta',
then it should offer any 'fasta' format files in the *current* history
as inputs when used.

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