Re: [galaxy-dev] Consuming dataset collections

2016-08-17 Thread John Chilton
Hey Steve - About sketching out some work on defining output collections this way: It took a while but I just got this pull request merged (https://github.com/galaxyproject/galaxy/pull/2697#issuecomment-240331966) which includes some fixes and examples for discovering datasets with galaxy.jso

Re: [galaxy-dev] Consuming dataset collections

2016-07-26 Thread Steve Cassidy
Hi John, thanks for the response. So based on your updated documentation I’ve modified my script to take the identifiers as a second argument and with a bit of juggling I now have the command line: query_textgrids.py --textgrid "${",".join(map(str, $textgrid))}" --identifier "${",".jo

Re: [galaxy-dev] Consuming dataset collections

2016-07-26 Thread John Chilton
Thanks for the questions - I have tried to revise the planemo docs to be more explicit about what collection identifiers are and where they come from (https://github.com/galaxyproject/planemo/commit/a811e652f23d31682f862f858dc792c1ef5a99ce). http://planemo.readthedocs.io/en/latest/writing_advanced

[galaxy-dev] Consuming dataset collections

2016-07-25 Thread Steve Cassidy
Hi all, I’m staring at the discussion of handling dataset collections: http://planemo.readthedocs.io/en/latest/_writing_collections.html but failing to see the solution to my problem. I have a tool that creates a dataset collection, a group of files with names like 1_1308_1_2_092-ch6-speaker