diff --git a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
index 69d3e32..69da29a 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
@@ -1,14 +1,10 @@
 package eu.neverblink.jelly.cli
 
 import caseapp.*
-import eu.neverblink.jelly.cli.JellyCommand.emptyRemainingArgs
 
 import java.io.{ByteArrayOutputStream, OutputStream, PrintStream}
 import scala.compiletime.uninitialized
 
-object JellyCommand:
-  val emptyRemainingArgs: RemainingArgs = RemainingArgs(Seq.empty, Seq.empty)
-
 abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
   private var isTest = false
   private var out = System.out
@@ -31,6 +27,17 @@ abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
       out = System.out
       err = System.err
 
+  /** Runs the command in test mode from the outside app parsing level
+    * @param args
+    *   the command line arguments
+    */
+  def runCommand(args: List[String]): (String, String) =
+    if !isTest then testMode(true)
+    osOut.reset()
+    osErr.reset()
+    App.main(args.toArray)
+    (osOut.toString, osErr.toString)
+
   def getOut: String =
     if isTest then
       out.flush()
@@ -51,24 +58,6 @@ abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
       s
     else throw new IllegalStateException("Not in test mode")
 
-  /** Run the command in test mode, capturing stdout and stderr.
-    * @param options
-    *   the command options
-    * @param remainingArgs
-    *   the remaining arguments
-    * @throws ExitError
-    *   if the command exits
-    * @return
-    *   (stdout, stderr)
-    */
-  @throws[ExitError]
-  def runTest(options: T, remainingArgs: RemainingArgs = emptyRemainingArgs): (String, String) =
-    if !isTest then testMode(true)
-    osOut.reset()
-    osErr.reset()
-    run(options, remainingArgs)
-    (getOut, getErr)
-
   @throws[ExitError]
   override def exit(code: Int): Nothing =
     if isTest then throw ExitError(code)
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
index e7721bd..bda172a 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
@@ -1,6 +1,5 @@
 package eu.neverblink.jelly.cli.command
 
-import caseapp.core.{Indexed, RemainingArgs}
 import eu.neverblink.jelly.cli.command.helpers.*
 import eu.neverblink.jelly.cli.command.rdf.*
 import org.apache.jena.riot.RDFLanguages
@@ -11,37 +10,34 @@ import scala.io.Source
 import scala.util.Using
 
 class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
+
   "rdf from-jelly command" should {
     "be able to convert a Jelly file to NTriples output stream" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = None)
-      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
       val (out, err) =
-        RdfFromJelly.runTest(
-          options,
-          args,
-        )
+        RdfFromJelly.runCommand(List("rdf", "from-jelly", jellyFile))
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
+
     "be able to convert a Jelly stream to NTriples output stream" in {
       DataGenHelper.generateJellyInputStream(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = None)
-      val (out, err) = RdfFromJelly.runTest(options)
+      val (out, err) = RdfFromJelly.runCommand(List("rdf", "from-jelly"))
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
     "be able to convert a Jelly file to NTriples file" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
-      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
       val nQuadString = DataGenHelper.generateNQuadString(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
-      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
-      val (out, err) = RdfFromJelly.runTest(options, args)
+      val (out, err) =
+        RdfFromJelly.runCommand(
+          List("rdf", "from-jelly", jellyFile, "--to", outputFile),
+        )
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted
       }
@@ -53,8 +49,8 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
       DataGenHelper.generateJellyInputStream(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
-      val (out, err) = RdfFromJelly.runTest(options)
+      val (out, err) =
+        RdfFromJelly.runCommand(List("rdf", "from-jelly", "--to", outputFile))
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted
       }
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/VersionSpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/VersionSpec.scala
index 3059933..aa88d2f 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/VersionSpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/VersionSpec.scala
@@ -6,7 +6,7 @@ import org.scalatest.wordspec.AnyWordSpec
 class VersionSpec extends AnyWordSpec, Matchers:
   "version command" should {
     "print something" in {
-      val (out, err) = Version.runTest(VersionOptions())
+      val (out, err) = Version.runCommand(List("version"))
       out should startWith("jelly-cli")
       out should include("Jelly-JVM")
       out should include("Apache Jena")