I want to be able to lower all windows and show the desktop from the command line, not
Ctrl+Alt+D.
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There is a useful command line application called xdotool
which amongst other stuff, allows you to send keystrokes.
Thus - to mimic Control+Alt+D (or Super+D, or whatever the combination is you need), you can use one of the following commands:
xdotool key ctrl+alt+d
xdotool key ctrl+super+d
xdotool key super+d
To install:
sudo apt-get install xdotool

Radu Rădeanu
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fossfreedom
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The key combination should not be quoted. Works as a charm. Thanks! – user42882 Jan 20 '12 at 22:09
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I'm not sure fossfreedom's answer truly satisfies the requirement to "not use Ctrl+Alt+D"
Thus I recommend to show desktop the command:
wmctrl -k on
To turn it off use
wmctrl -k off

virtualxtc
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