Documents may be uploaded via the REST API or by using the One Codex CLI or Python client library. The latter two options are simpler and thus recommended. In every case, we replace spaces in filenames with underscores. To upload with the CLI, simply: 
# If you haven't previously logged in, the following command
# will prompt you for your username and password and then
# save a ~/.onecodex file with your API key
onecodex login

onecodex documents upload $LIST_OR_GLOB_OF_YOUR_DOCUMENTS
Uploading via the REST API consists of 3 steps:

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Documents over 20GB

The above upload mechanisms currently only allow document uploads up to 20GB (optionally compressed with gzip). If you need to upload a compressed file over 20GB, please contact us at support@onecodex.com and we can provide an alternative upload or file import mechanism for your situation.