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 upload? 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. Peter On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
I am trying to import a file into galaxy.
On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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 format.
Which of these are you trying to do? Or both?
Peter
On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu <katherine.beaulieu014@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@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@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 know if you would like to see my tool config file. Cheers, Katherine
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