You must apply plugin: 'scalajs-plugin' and declare

buildscript {
    repositories {
        mavenCentral()
    }
    dependencies {
        classpath 'com.github.gtache:scalajs-plugin:sjs[scalaJSVersion]_[scalaVersion]_0.3.0'
    }
}

to use this plugin.
(With scalaJSVersion '0.6' and scalaVersion '2.12', that would be 'scalajs-plugin:sjs0.6_2.12_0.3.0')
Check the build.gradle of scalajs-plugin-test if needed.
Needs .scala files to be in src/main/scala (or configure your ScalaCompile task accordingly)
Needs tests to be in src/test/scala.

This plugin adds :
-apply plugin: 'java'
-apply plugin: 'scala'
and dependencies on scalajs-library (version depending on plugin version), scalajs-compiler (version depending on plugin version), as well as org.eclipse.jetty:jetty-server:8.1.16.v20140903 and org.eclipse.jetty:jetty-websocket:8.1.16.v20140903 for PhantomJS

gradlew FastOptJS, gradlew FullOptJS or gradlew NoOptJS to compile everything.

You can run the generated javascript file with gradlew RunJS.
You can run tests with gradlew TestJS. Be aware that this is still an early feature.
You can read the sjsir files with gradlew Scalajsp.

-ScalaTest
-JUnit (you have to add the junit-test-plugin to the compileTestScala task)
-Minitest
-utest (not fully supported, the summary will print the tests as Unknown and the retest feature will ignore them)
-ScalaProps
You can mix them (Have a JUnit suite with a utest suite and a ScalaTest suite, etc)
You must obviously add the dependencies and TestFrameworks for those to work.

To add the JUnit plugin or the dependencies, please refer to the build.gradle in scalajs-test-plugin.

--Po="pathtofile" | -Poutput="pathtofile" to change where the js file will be generated This means that there will only be one file for every different build (fast, full, test or not)
--Pp | -Pprettyprint for prettyPrint
--Ps | -Psourcemap for sourceMap
--PcompliantAsInstanceOfs
--Pm=NameOfMode | -PoutputMode=NameOfMode to change the output mode (ECMAScript51Global, ECMAScript51Isolated, ECMAScript6)
--Pc | -PcheckIR
--Pr="PathToSourceMap" | -PrelativizeSourceMap="PathToSourceMap" to add a sourceMap
--PlinkLogLevel=Debug|Info (default)|Warn|Error to change the level of logging
--Pd | -Pdebug for Debug level
--Pq | -Pquiet for Warn level
--Pqq | -Preally-quiet for Error level
--Pbatch to turn on batch mode
--PnoParallel to set parallel to false

--Pclassname is the fully qualified name of the class to run
--Pmethname is the method of classname to run.
--PtoExec (has higher priority than -Pclassname) will run the given explicit command
--PfileToExec (has highest priority) will run the given js file.
-Adding -PrunNoOpt will run the unoptimized file
-Adding -PrunFull will run the fully optimized file
-It will run the fast optimized file by default.
RunJS will depend on FastOptJS (default), FullOptJS or NoOptJS accordingly.
-Adding -Pphantom will run the file in a phantomjs environment (needs phantomjs on path).
-Adding -Prhino will run the file in a rhino environment.
-Adding -PjsDom will run the file with Node.js on a JSDOM window.
-You can change the level of logging with -PrunLogLevel=Warn for example.
-You can add java system properties with '-PjavaOpt="-D=;=;..." (replace semicolon with colon if you are on an Unix system)

Examples : gradlew RunJS -Pclassname="main.scala.DummyObject" will compile everything and run DummyObject().main()

gradlew RunJS -Pclassname="main.scala.DummyObject" -Pmethname="printSomething(\"blabla\")" -PrunFull will compile the fully optimized version of the files and will run DummyObject().printSomething("blabla")

gradlew RunJS -PtoExec="main.scala.DummyObject().main() -Pphantom" will compile everything and run DummyObject().main() in a phantomjs environment.

gradlew RunJS -PfileToExec="testjs/TestRunWithFile.js" will run TestRunWithFile.js with the environment loaded with the compiled js file.

--PrunFull, -PrunNoOpt, -Pphantom, -PjsDom and -Prhino have the same behavior as with RunJS.
--Ptest-only=class1;class2;*l*s3 and --Ptest-quick=... should have the same behavior as their sbt counterparts. You can only select classes / suites at the moment, you can't select tests.
--Pretest should retest all failed tests (does not work with Utest).
You can change the level of logging with -PtestLogLevel=Error for example.
Note that retest / test-quick need a Gradle daemon to work.

--Ps | -Psupported will display the supported sjsir versions
--Pi | -Pinfo will display informations about the file(s)
--Pf | -Pfilename to choose which file(s) to see (eg : 'build/classes/main/com/github/gtache/DummyObject$.sjsir')
--Pj | -Pjarfile to choose a jar

Don't forget that you can set the options directly in build.gradle. Simply put the property in the 'ext' closure.
Example : Instead of writing -PtestLogLevel=Debug -Po="generated.js" -Pd -PfileToExec="toExec/exec.js" everytime, write

ext {    
    testLogLevel="Debug" //Use a string
    o="generated.js"
    d=true //or false, or whatever, it just checks that the property exists
    fileToExec="toExec/exec.js"
    testFrameworks=["utest.runner.Framework","minitest.runner.Framework"] //If you need to add TestFrameworks
}

-Permission denied
=> Solution : apply chmod +x to gradlew
-GC overhead limit exceeded when running CompileJS
=> Solution : edit gradle.properties in %USER%/.gradle/ with org.gradle.jvmargs=-Xmx4096m -XX:MaxPermSize=4096m -XX:+HeapDumpOnOutOfMemoryError (or tweak the numbers) (source : http://stackoverflow.com/questions/27164452/how-to-solve-java-lang-outofmemoryerror-gc-overhead-limit-exceeded-error-in-and)
(Don't forget to delete the hprof file in the project folder)
-Something related to the linker state, after a failure while linking
=> Solution : gradlew --stop to stop the daemon containing the linker. Then rerun the desired command as usual. (This problem should be fixed now)

###0.3.0 (uses Scala 2.12.1 or Scala 2.11.8 with scalajs 0.6.15)
-Updates to Scala 2.12 and Scalajs 0.6.15
-Adds Scalajsp
-Adds JSDOMNode environment
-Adds custom environment option
-Adds custom semantics option
-Adds custom OptimizerOptions option
-Adds batchMode, parallel
-Adds Java system properties
-Various improvements / bugfixes

###0.2.0 (uses Scala 2.11.8 with scalajs 0.6.9)
-Adds support for RhinoJS and PhantomJS
-Adds options for the linker
-Removes useless tasks
-Adds support for basic testing
-Various improvements (cleaning, bugs, etc)

###0.1.1 (uses Scala 2.11.8 with scalajs 0.6.9)
-Adds -PtoExec to input directly what to execute.
-Linker and Cache are kept alive (should increase speed dramatically). Only works with a gradle daemon.
-Fixes a problem with the linker not linking when files are changed.

###0.1.0 (uses Scala 2.11.8 with scalajs 0.6.9)
-First version