  #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

Stiftingtalstraße 24

8010 Graz, Austria

mina.bashir@medunigraz.at

+43 (0) 316 385 72713

Am 19.06.2016 um 00:51 schrieb Nikolaos Tur <nikolaos.tur@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.bashir@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.tur@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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