OK. What happens?
Can you select the correct datatype in the upload tool?
If not, check the file format definition as some file formats
are configured not to appear here.
Are you leaving the datatype as "auto"? If so, does
Galaxy fail to identify the file, and leave it as the
default generic "data" type, or does Galaxy mis-identify
it as another type?
Have you looked at the Galaxy logs while doing the
How is this file format defined in Galaxy? Did you add it?
Can you test the Python code in the sniff function outside
of Galaxy to confirm that works?
If Galaxy wrongly picks another fileformat, check where
in the datatypes_conf.xml is your file format listed? The
order the sniffing functions are run is important.
On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu
I am trying to import a file into galaxy.
On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.cock(a)googlemail.com>
> The auto-detection is only used when importing a
> file into Galaxy (e.g. by uploading it).
> If you are writing a tool which produces output in your
> format, then the tool's XML should specify that output
> Which of these are you trying to do? Or both?
> On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu
> <katherine.beaulieu014(a)gmail.com> wrote:
> > Hmm, I must have some sort of other logic error which is preventing the
> > detection of the format. Thanks for the information!
> > On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.cock(a)googlemail.com>
> > wrote:
> >> Have you invented your own file format, or are you using
> >> an existing file format defined within Galaxy?
> >> The Galaxy file formats with automatic detection are all
> >> defined via Python classes which define a sniff method.
> >> Peter
> >> On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu
> >> <katherine.beaulieu014(a)gmail.com> wrote:
> >> > Hi everyone,
> >> > I am looking to auto-detect the file format of a file outputted by a
> >> > python
> >> > tool I have written. Does anyone have any idea how to do this? I have
> >> > tried
> >> > setting the format attribute to "auto" with no luck. Let me
> >> > you
> >> > would like to see my tool config file.
> >> > Cheers,
> >> > Katherine
> >> >
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