Hi,
You can solve the extension issue using soft links in your tool wrapper. 
E.g.:
ln -s $input_fasta $input_fasta.fna

Best,
Mina

Sent from my iPhone

> On Jun 18, 2016, at 12:04, Nikolaos Tur <nikolaos....@gmail.com> wrote:
> 
> Hi,
> 
> does someone use latest version of flexbar 2.7 with Galaxy? It seems newest 
> flexbar changes way how it works with data. Now it requires format extension 
> for data. But Galaxy operates data with .dat extension in database/files/.
> Also there is flexbar wrapper for version 2.7, so it should be somehow 
> integrated to the Galaxy. Our Galaxy is 16.04.
> 
> Thanx,
> Nikolaos
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