Using a collection [from a list of collections] as tools input

[cumbof]

Currently it is not possible to use a collection as input for any tool if this collection is inside a list of collections. I have encountered this problem for the tool referring to the pull request #1380 under the tools-iuc repository. The output of the tool is the following:

<collection name="list_output" type="list:list" label="${tool.name} Output Collection">
        <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)_(?P&lt;dbkey&gt;[^_]+)" ext="auto" visible="False" directory="tmp" />
</collection>

@nekrut @jmchilton

[nekrut]

@jmchilton when you are here, can you talk to @fabio-cumbo about this?

[jmchilton]

@fabio-cumbo Here is the related issue I was talking about I think - #740. If you are interested in maybe trying to extend Galaxy to allow tools to output multiple collections at runtime - create another issue and I can try to flush out how to do that - but I'm not sure I'd have time to work on it myself.

[cumbof]

Thanks @jmchilton!

[jmchilton]

If you are interested in maybe trying to extend Galaxy to allow tools to output multiple collections at runtime - create another issue and I can try to flush out how to do that - but I'm not sure I'd have time to work on it myself.

This part - allowing a dynamic number of collections - is included in #5220. If anyone is interested in writing a tool that would do this I can document how to do that as part of the PR or in a follow up.

[cumbof]

Thanks @jmchilton, it would be great if this will be documented

[mvdbeek]

I think this works for a while now, and if not 19.01 should work.