Yes - let’s say you have hard coded paths… you could put those into a select 
list pretty easily (just have the paths embedded like the bowtie wrapper does 
the paired-end vs. single-end select list).

You might also want to consider a table lookup though.
The bowtie wrapper does that for reference genomes.
You can make your own lookup table to refer to whatever files you want, which 
would allow you to update paths without installing new version of the tool.

Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs

On Aug 26, 2016, at 1:06 PM, Katherine Beaulieu 
<katherine.beaulieu...@gmail.com<mailto:katherine.beaulieu...@gmail.com>> wrote:

Hi Brad,
So with multiple selection dropdown lists this is possible? Do you have an 
example of a tool that can do this? Would it be possible to see an example of 
the tools you are talking about? Thanks for the help!

On Fri, Aug 26, 2016 at 12:05 PM, Langhorst, Brad 
<langho...@neb.com<mailto:langho...@neb.com>> wrote:
Hi Katherine:

I’d recommend not having users type in paths if at all possible (they will make 
frustrating mistakes).
If there is a selection of these maybe consider turining them into dropdown 

Either way,  these would be no different than e.g. user specified downsampling  
amounts. or library names, etc.
I have tools that accept many of these.


Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs

On Aug 26, 2016, at 10:57 AM, Katherine Beaulieu 
<katherine.beaulieu...@gmail.com<mailto:katherine.beaulieu...@gmail.com>> wrote:

What if its multiple file paths that the user types in rather than actual 
files, which makes it so the tool can't be executed in batch mode, would it 
still be workflow compatible at that point? Thanks for pointing me to the 
Bowtie wrappers as an example.

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