Is there a way to define base link in urdf file

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You probably want to change the configured value for the Fixed Frame and set it to one of the frames in your TF tree.

Is there away to do that from the command line at start?

have you checked the RViz help?

rviz command line options:
  -h [ --help ]               Produce this help message
  -s [ --splash-screen ] arg  A custom splash-screen image to display
  --help-file arg             A custom html file to show as the help screen
  -d [ --display-config ] arg A display config file (.rviz) to load
  -f [ --fixed-frame ] arg    Set the fixed frame
  -l [ --ogre-log ]           Enable the Ogre.log file (output in cwd) and 
                              console output.
  --in-mc-wrapper             Signal that this is running inside a 
                              master-chooser wrapper
  --opengl arg                Force OpenGL version (use '--opengl 210' for 
                              OpenGL 2.1 compatibility mode)
  --disable-anti-aliasing     Prevent rviz from trying to use anti-aliasing 
                              when rendering.
  --no-stereo                 Disable the use of stereo rendering.
  -v [ --verbose ]            Enable debug visualizations
  --log-level-debug           Sets the ROS logger level to debug.

You can use the --fixed-frame argument.

Note that it will also be saved as part of your RViz configuration, so after setting it once, save the configuration as part of your package and you don't need to use the CLA.