Hi Folks,
thank you so far for the previous help. I got much further. Now I'm stuck with data collections.
Because this is quite a list, I appreciate also answers to parts of my questions ;)
I have two issues: A) manual definition of data collections (any type) by user and/or admin B) definition of data collections as input/output of a tool and inside a workflow
A) manual Basically I would like to create i) a list of fastq files (unpaired) ii) a paired set of two fastq files iii) a list of each two paired fastq files
How can I do that? By using the web app? As user? As admin? By working via ssh on the server?
B) in tool/workflow Here I also have different approaches I would like to realize: i) use a collection as input for a tool ii) create a collection as output of a tool ii.1) from known # of output parameters ii.2) from unknown # of output parameters
For these things I was trying to find some tools in toolshed to see how they do it, but I couldn't quite adopt it.
i) use a collection as input for a tool this is good documented - realizable by type="data_collection" and the collection_type. Unfortunately I can't test this because I can't create a collection so far ;) - see A
ii) create a collection as output of a tool Here it gets blurry for me.
ii.1) from known # of output parameters Here I didn't find a tool. I just thought, it might be a simpler case than ii.2 and good to understand the concept. I would be glad if someone could explain the way(s) to do this.
ii.2) from unknown # of output parameters For this I found barcode splitter tools (also from devteam) that have different approaches. But. Their output (defined in xml) is only some report file. The output files seem to be fed into the history. And here I don't know how to get hands on these files when I want to use them to feed them into the next step during a workflow.
Help highly appreciated!
Thanks! Alexander