Hi Nikolaos,
Exactly, you need to change your too.xml file. You could try to solve this with 
an if condition:

  #if isinstance($input_fasta.datatype, 
$__app__.datatypes_registry.get_datatype_by_extension('fastq').__class__):
   ln -s $input_fasta $input_fasta.fastq
  #elif isinstance($input_fasta.datatype, 
$__app__.datatypes_registry.get_datatype_by_extension('fasta').__class__):
   ln -s $input_fasta $input_fasta.fastq
  
## use as many elifs as you need

  #else:
   ln -s $input_fasta $input_fasta.fastq.gz
  #end if

Might not be the most elegant way, but I think it should work, assuming that 
you have added all extensions to datatypes.

best,
Mina

Mina Bashir, MSc
Division of Endocrinology & Diabetology
Medical University of Graz
ZMF Center for Medical Research
Stiftingtalstra├če 24
8010 Graz, Austria
mina.bas...@medunigraz.at <mailto:mina.bas...@medunigraz.at>
+43 (0) 316 385 72713




> Am 19.06.2016 um 00:51 schrieb Nikolaos Tur <nikolaos....@gmail.com>:
> 
> thanx Mina, I thought about this. If no one still did this, question is where 
> to add soft link creation.
> Probably in flexbar.xml. Now flexbar supports fasta and fastaq format, also 
> their gziped/bziped versions.
> How to determine data format in Galaxy? I'm not an expert neither in Galaxy 
> nor biology, just try to administrate
> Galaxy instance.
> 
> Thanx,
> Nikolaos
> 
> On Sat, Jun 18, 2016 at 2:54 PM, Mina Bashir <mina.bas...@medunigraz.at 
> <mailto:mina.bas...@medunigraz.at>> wrote:
> 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 
> > <mailto: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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> 

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