Karma/Mocha unit tests with ES2015+ preprocess without launching the app - ecmascript-6

Question

I have an existing front js application without any unit tests. It's not actually particularly suitable for all sources to be unit tested (no dependency injection, not decoupled in units, DOM manipulation heavily mix with logic, etc.) but some files (ES2015 modules) can be right now testable.
I decided to go with Karma/Mocha/Chai and i already have a standalone karma test which works with the following configuration.
module.exports = function(config) {
config.set({
basePath: '',
frameworks: [
'mocha',
'chai',
],
singleRun: true,
files: [
'node_modules/babel-polyfill/dist/polyfill.js',
'src/**/*.js',
],
preprocessors: {
'src/**/*.js': ['babel'],
},
babelPreprocessor: {
options: {
presets: ['es2015'],
plugins: ['transform-es2015-modules-umd'],
sourceMap: 'inline',
},
},
browsers: [
'Chrome',
//'ChromeCanary',
//'PhantomJS',
//'Firefox',
//'Opera',
//'IE',
//'Safari',
],
reporters: [
'mocha',
],
});
};
my structure files is as follow :
node_modules
src/
module.js
module.test.js
karma.conf.js
package.json
the package.json have this dependencies :
"devDependencies": {
"babel-core": "^6.26.0",
"babel-plugin-transform-es2015-modules-umd": "^6.24.1",
"babel-polyfill": "^6.26.0",
"babel-preset-es2015": "^6.24.1",
"chai": "^4.1.2",
"karma": "^1.7.1",
"karma-babel-preprocessor": "^7.0.0",
"karma-chai": "^0.1.0",
"karma-chrome-launcher": "^2.2.0",
"karma-firefox-launcher": "^1.0.1",
"karma-growl-reporter": "^1.0.0",
"karma-ie-launcher": "^1.0.0",
"karma-mocha": "^1.3.0",
"karma-mocha-reporter": "^2.2.4",
"karma-opera-launcher": "^1.0.0",
"karma-phantomjs-launcher": "^1.0.4",
"karma-safari-launcher": "^1.0.0",
"mocha": "^4.0.0"
}
And just for easy usage :
"scripts": {
"test": "karma start"
},
Now i'm trying to integrate that configuration with the existing project, but it's failing because it runs all sources on the browser, so trying to bootstrap the app without the dependencies (external scripts). But even if I include all those in the 'file' config property of karma, there will be always problems with DOM manipulation on not existing HMTL, relying on global variables not here, etc.
So I'm wondering how to preprocess (logically and with what tools) to have only my *.test.js to be launched without my app bootstrapping. And so to load only the files needed for the tests.
I was thinking of making a bundle for each *.test.js file with the corresponding file tested (resolved with the import), and this way, as far as i don't make test files for all files not ready to be tested in my app, they should not be loaded.
Is this the best way to go, how can the tests can be done in an other way ?