I'm glad you could solve this - thanks for letting us know and
linking to the old email discussion which helped.
Peter
On Thu, Jul 7, 2016 at 4:35 PM, Katherine Beaulieu
wrote:
> Hi Peter, I ending up finding a solution to my problem using this forum
> post:
> https://lists.galaxyproject.org/pip
Hi Peter, I ending up finding a solution to my problem using this forum
post:
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html.
I just ended up using the really specific file output path and it started
auto-detecting the file format. Thanks for your help it was much
appr
Hi Katherine
I presume this is related to the tool described here (
https://biostar.usegalaxy.org/p/18319/)? I think there is general interest
in the creation of a tool like this - see the recent email from Miu ki Yip.
If you could share the code and XML (e.g. via GitHub) perhaps we could
assist w
Maybe sharing your tool XML file would be best - is it on GitHub?
Peter
On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu
wrote:
> Ok, so I don't give the user the option to select the correct data type to
> reduce the amount of stuff the user has to know when using the tool.
>
> I do leave th
Ok, so I don't give the user the option to select the correct data type to
reduce the amount of stuff the user has to know when using the tool.
I do leave the format as auto and Galaxy just leaves it as the generic data
type 'data'.
As for how the format is defined in Galaxy, I'm not quite sure w
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 "dat
I am trying to import a file into galaxy.
On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock
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 tha
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, K
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
wrote:
> Have you invented your own file format, or are you using
> an existing file format defined within Galaxy?
>
> The Gal
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
wrote:
> Hi everyone
Hi Katherine,
The file datatype have support on galaxy plataform!? If not, you add the
datatype what you need in your galaxy instance!?
Att.
On Wed, Jun 29, 2016, 11:16 AM Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi everyone,
> I am looking to auto-detect the file format of
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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