Collection are one potential answer for how users can specify the set of stuff that belongs in the directory. For explicitly dealing with applications that consume directories - I think it is best to just create the directory and link in files (if possible) before the tool runs. <command>mkdir input_dir; #for $i, $input_file in enumerate($input_files)# ln -s "$input_file" "input_dir/$i"; #end for my_application input_dir </command> <inputs> <param name="input_files" type="data" format="bam" multiple="true" /> ... You can also do this sort of thing in a wrapper. If needed you can build more interesting command-lines this way that add extensions, use names, etc.... peptideshaker is an example of a fairly complex tool that uses an idiom like this and doesn't resort to a helper wrapper (https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=13a5bad5c984d...). I am currently working on support for tools that actually produce collections of files this way - I think I will probably land up adding some high-level utilities for doing stuff like this for those scenarios. But if you tool just produces a couple files and consume a directory - no need to necessarily resort to collections (as the tool author - your users will probably want to if they want to use these tools in workflows). -John On Tue, Sep 2, 2014 at 9:51 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

You might be able to do this by accepting a collection of SAM/BAM files as input instead. This is a quite new feature in Galaxy, see:

https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution

Peter

On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet <philippe.mcqt@gmail.com> wrote:

...

Hi,

I am trying to write a wrapper for a tool that take a directory containing SAM/BAM files as an input. I am not sure how to do that, is there another tool that implements this and that I can have a look at ? Any suggestions would be greatly appreciated.

Regards, Philip

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