I think introducing a new a type like mutect.fasa or something is
probably the better idea here. You can create a tool that creates this
datatype and your main mutect tool wrapper can then take an input of
type <param name="input" type="data" format="fasta,mutect.fasta"...
and only re-index when a vanilla fasta is passed in.
If you did modify the existing fasta datatype - those changes would
not really be pulled in as part of tool shed installs say - and I
would be hesitant to collect extra metadata for every fasta datatype
in the core code for a single application.
Hope this helps,
On Thu, Jan 15, 2015 at 1:03 PM, Marco Albuquerque
> Hello Galaxy,
> I have a small dilemma regarding the fasta datatype.
> Currently, to my knowledge, the fasta datatype does not specify any
> metadata. I was curious how I should go about changing the fasta datatype if
> I wanted to include the .fai and .dict as metadata? Basically I want to
> avoid unnecessary recreating of the same file done automatically by MuTect.
> It seems very inefficient to have to produce these files every time a user
> were to call MuTect in galaxy (I.e. MuTect can't find them, so it makes them
> I guess my question is, what are the consequences to adjusting the current
> implementation of the fasta datatype? Will users be able to pull this tool
> easily? (I.e. When one uploads a tool and that tools uses a different fasta
> definition, how does galaxy handle this?) Could this new fasta declaration
> potentially be adapted by galaxy? Should I just define a new mtfasta
> datatype special for MuTect purposes?
> Let me know if you have any advice,
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