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

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,
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
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