Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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: >

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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,