I am trying to configure a new tool in my instance of galaxy. The tool itself creates a bunch of output files. However, when I run this tool through the galaxy instance, it still creates a folder with all the files in its own directory ( as it does when you run the tool by itself from the command line ). As a results, the output files are not accessible by Galaxy. 

Is there any way I can configure galaxy to read the entire contents of the output directory or redirect my tool to create the output files in galaxy's default output directory while reading all of them as outputs? 

Thanks a ton in advance, 

K