Re: [galaxy-dev] Multiple outputs of unknown types

2015-04-08 Thread John Chilton 
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 davidke...@uchicago.edu 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

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Re: [galaxy-dev] Multiple outputs of unknown types

2015-04-08 Thread 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 jmchil...@gmail.com 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 davidke...@uchicago.edu 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
 
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[galaxy-dev] Multiple outputs of unknown types

2015-04-01 Thread 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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