Can I upload data (mostly link the data) using terminal ?

MuSiC 2 tool integration is not available in their website nor in tool shed.

MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy.

So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2.

ex: if you run  

                music2   bmr     calc-bmr    file_of_input

output is 3 files,

./file1.txt

./folder1/file2.txt

./folder2/file3.txt

we can not mention that we need this output filename or save file at specific location, we can not give this option.

Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ?

Waiting for positive reply.

Thank You

- Chetan