WebStorm run npm script in tool window (Protractor)

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I would like to be able to run an npm script in the Protractor tool window rather than npm. This is easily doable creating a new Protractor Run/Debug config but I need to add a command line argument which the Run config doesnt currently support.

More specifically I am trying to run

protractor --capabilities.chromeOptions.args=--headless --capabilities.chromeOptions.args=--disable-gpu

Would like to do this without modifying the protractor config file.

Essentially, I want to be able to do this without having to provide multiple config files in my project. One for headless, one without.

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There is currently no way to specify cmd options in Protractor run configuration, please follow WEB-25165 for updates