Hello Jun, See my answers inline. On Wed, May 21, 2014 at 10:34 AM, Jun Fan <j.fan@qmul.ac.uk> wrote:

Dear all,

I have a tool which generates dynamic number of mzid outputs depending on the number of selected files and tools ( = number of files * number of tools). The suggested methods to deal with this situation are 1) composite html which contains links to all outputs or 2) put output files in the $__new_file_path__ with some naming convention. Neither of these can specify the output type of the tool to the desired value “mzid”, which makes it impossible to connect this tool to the downstream tool taking mzid as input. My solution to this is to limit to single file selection, then listing all possible mzid output files with filter elements. I am wondering whether there is better solution to solve this.

I think given the current state of Galaxy this is how I would proceed. It sounds like the underlying application might be better represented by one Galaxy 'tool' per method? That may not be feasible if the methods are not independent - but it is something to consider - there are many applications that are represented by multiple Galaxy tools. We are actively working on adding functionality for dealing more intelligently with groups of files. A summary of the parts that will be added to the next release and links to Trello cards to flush out more of our plans can be found in the following presentation: https://docs.google.com/presentation/d/12kcpKh6osgh3H8iqTnnr9MDDx-yNSal-Fa9Q...

Another question about workflow: if a tool A can generate two types of output: C and D, and another tool B can take type C, D and E as its input, it is fine to connect these two tools A and B in the workflow. However, if the types selected for input and output do not match (e.g. type C for tool A output and type D for tool B input or even type E), how to configure galaxy to spot this inconsistency?

There is no way to configure Galaxy currently to catch this inconsistency. I certainly think it should be possible for Galaxy to do a better job and I have created a Trello card for this feature request here - https://trello.com/c/MaiLqXHP - feel free to vote on it. -John

Best regards!

Jun

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