diff --git a/tests/test_run_emmtyper.py b/tests/test_run_emmtyper.py
new file mode 100644
index 0000000..d9dfde4
--- /dev/null
+++ b/tests/test_run_emmtyper.py
@@ -0,0 +1,39 @@
+"""
+Test the command line intereface
+"""
+
+from click.testing import CliRunner
+from emmtyper.bin.run_emmtyper import main
+from emmtyper import __version__ as version
+
+from tests.data import test_sequence_path
+
+
+runner = CliRunner()
+
+
+def test_run_emmtyper_version():
+    """
+    Test emmtyper --version flag
+    """
+    result = runner.invoke(main, ["--version"])
+    assert result.exit_code == 0
+    assert result.output == f"emmtyper v{version}\n"
+
+
+def test_run_emmtyper_basic_blast():
+    """
+    Test basic blast workflow
+    """
+    result = runner.invoke(main, [test_sequence_path])
+    assert result.exit_code == 0
+    assert result.output == "contig.tmp\t1\tEMM1.0\t\tA-C3\n"
+
+
+def test_run_emmtyper_basic_ispcr():
+    """
+    Test basic ispcr workflow
+    """
+    result = runner.invoke(main, ["-w", "pcr", test_sequence_path])
+    assert result.exit_code == 0
+    assert result.output == "contig_pcr.tmp\t1\tEMM1.0\t\tA-C3\n"