Multiple outputs of unknown types

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Multiple outputs of unknown types

David Kelly
Hello,

I've looked through the documentation about tools that produce multiple output files, but it seems like you're required to know the data types ahead of time (or make assumptions based on input data). But what about a case where you don't know what the output datatypes will be? Is it just possible to have N output files imported and sniffed?

Thanks,
Davids

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Re: Multiple outputs of unknown types

John Chilton-4
I had my own use case for this a few weeks ago and I couldn't figure
out anyway to configure this right now - I was hoping Dan might
respond to your question with some crazy trick though. For now I have
created a Trello card for the implementation of this feature - please
vote for it:

https://trello.com/c/FZ67pAAE

-John


On Wed, Apr 1, 2015 at 7:29 PM, David Kelly <[hidden email]> wrote:

> Hello,
>
> I've looked through the documentation about tools that produce multiple
> output files, but it seems like you're required to know the data types ahead
> of time (or make assumptions based on input data). But what about a case
> where you don't know what the output datatypes will be? Is it just possible
> to have N output files imported and sniffed?
>
> Thanks,
> Davids
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: Multiple outputs of unknown types

Daniel Blankenberg
Hi Davids,

For some a somewhat more complex example, have a look at the GenomeSpace importer tools under tools/genomespace in the distribution. They always create at least 1 dataset, but can create any number of files, of any type of datatype. In this tool, it will use the filetype declared by GenomeSpace, or it will fall back to using Galaxy’s sniffing functions of it doesn’t know the datatypes.

This makes use of the ‘galaxy.json’ file —> json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE']


Thanks,

Dan


On Apr 8, 2015, at 9:24 AM, John Chilton <[hidden email]> wrote:

I had my own use case for this a few weeks ago and I couldn't figure
out anyway to configure this right now - I was hoping Dan might
respond to your question with some crazy trick though. For now I have
created a Trello card for the implementation of this feature - please
vote for it:

https://trello.com/c/FZ67pAAE

-John


On Wed, Apr 1, 2015 at 7:29 PM, David Kelly <[hidden email]> wrote:
Hello,

I've looked through the documentation about tools that produce multiple
output files, but it seems like you're required to know the data types ahead
of time (or make assumptions based on input data). But what about a case
where you don't know what the output datatypes will be? Is it just possible
to have N output files imported and sniffed?

Thanks,
Davids

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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 http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

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 http://galaxyproject.org/search/mailinglists/



___________________________________________________________
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