Unofficial way of doing this and the workaround of using configfiles can be found in this thread: http://dev.list.galaxyproject.org/Simple-standard-for-API-use-of-a-global-user-key-that-all-loaded-tools-can-draw-upon-td4665659.html. There is a Trello card outlining platform work that should be done to support this better but we have not made progress on that.
I would be interested in your use case. One can dynamically discover datasets with various db keys and build collections composted of dynamically discovered datasets and keys - but there is no way to use the tool xml to dynamically discover a variable number of collections - but it should be supported - as should building a list of paired or lists of lists where the outer list describes the key and the inner the sample. -John On Wed, Apr 29, 2015 at 2:58 PM, Ben Bimber <bbim...@gmail.com> wrote: > Hello, > > I am new to galaxy. I"m trying to write a data input tool wrapper. It will > call a script that does a query, produces a list of files, and then the plan > is to use the BioBlend API to create datasets/data collections in galaxy. > In other words I am making the dataset(s) based on the contents of this > file, rather than making a dataset from that file. In my case this file has > a pair of columns representing FASTQ files, and I want to create one paired > dataset collection in galaxy for each genome. > > In theory using bioblend to create datasets is easy. However, when I call > this as a galaxy tool, I have not found a clean way to pass the credentials > to bioblend. BioBlend needs to know the serverURL and either the user's API > key or username/password. I think if I poke around $__app__ or $__user__ > there's a good change I will find a property with the information I need; > however, this has the obvious problem of writing the API key to the log. > > Is there another way to approach this problem? > > Thanks in advance for any help, > Ben > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
