--- a
+++ b/tests/test_cli.py
@@ -0,0 +1,201 @@
+import sys
+import warnings
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from wsic import cli
+
+
+def test_convert_timeout(samples_path, tmp_path):
+    """Check that CLI convert raises IOError when reading times out."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        warnings.simplefilter("ignore")
+        with pytest.raises(IOError, match="timed out"):
+            runner.invoke(
+                cli.convert,
+                ["-i", in_path, "-o", out_path, "--timeout", "0"],
+                catch_exceptions=False,
+            )
+
+
+def test_thumbnail(samples_path, tmp_path):
+    """Check that CLI thumbnail works."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-s", "512", "512"],
+            catch_exceptions=False,
+        )
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_thumbnail_downsample(samples_path, tmp_path):
+    """Check that CLI thumbnail works with downsample option."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        result = runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-d", "16"],
+            catch_exceptions=False,
+        )
+        assert result.exit_code == 0
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_thumbnail_no_cv2(samples_path, tmp_path, monkeypatch):
+    """Check that CLI thumbnail works without OpenCV (cv2)."""
+    monkeypatch.setitem(sys.modules, "cv2", None)
+    with pytest.raises(ImportError):
+        import cv2  # noqa # skipcq
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC.jp2"
+        out_path = Path(td) / "XYC.jpeg"
+        runner.invoke(
+            cli.thumbnail,
+            ["-i", str(in_path), "-o", str(out_path), "-s", "512", "512"],
+            catch_exceptions=False,
+        )
+        assert out_path.exists()
+        assert out_path.is_file()
+        assert out_path.stat().st_size > 0
+
+
+def test_help():
+    """Test the help output."""
+    runner = CliRunner()
+    help_result = runner.invoke(cli.main, ["--help"])
+    assert help_result.exit_code == 0
+    assert "Console script for wsic." in help_result.output
+
+
+def test_transcode_svs_to_zarr(samples_path, tmp_path):
+    """Test the CLI for transcoding SVS to zarr."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region.svs")
+        out_path = str(Path(td) / "CMU-1-Small-Region.zarr")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_svs_to_tiff(samples_path, tmp_path):
+    """Test the CLI for transcoding SVS to (tiled) TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region.svs")
+        out_path = str(Path(td) / "CMU-1-Small-Region.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_dicom_to_tiff(samples_path, tmp_path):
+    """Test the CLI for transcoding DICOM to (tiled) TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region")
+        out_path = str(Path(td) / "CMU-1-Small-Region.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_convert_jp2_to_tiff(samples_path, tmp_path):
+    """Test the CLI for converting JP2 to tiled TIFF."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        result = runner.invoke(
+            cli.convert,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_convert_jp2_to_zarr(samples_path, tmp_path):
+    """Test the CLI for converting JP2 to zarr."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.zarr")
+        result = runner.invoke(
+            cli.convert,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+
+def test_transcode_bad_input_file_ext(samples_path, tmp_path):
+    """Test the CLI for transcoding with a bad input file extension."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        # in_path must exists but not be a valid input
+        in_path = str(samples_path / "XYC.jp2")
+        out_path = str(Path(td) / "XYC.tiff")
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", in_path, "-o", out_path],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 2
+
+
+def test_transcode_bad_output_file_ext(samples_path, tmp_path):
+    """Check that CLI raises click.BadParameter when output file extension is bad."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = samples_path / "XYC-half-mpp.tiff"
+        out_path = Path(td) / "XYC.foo"
+        result = runner.invoke(
+            cli.transcode,
+            ["-i", str(in_path), "-o", str(out_path)],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 2
+
+
+def test_convert_svs_to_zarr_zip(samples_path, tmp_path):
+    """Test the CLI for converting SVS to zipped zarr."""
+    runner = CliRunner()
+    with runner.isolated_filesystem(temp_dir=tmp_path) as td:
+        in_path = str(samples_path / "CMU-1-Small-Region.svs")
+        out_path = str(Path(td) / "CMU-1-Small-Region.zarr.zip")
+        result = runner.invoke(
+            cli.convert,
+            ["-i", in_path, "-o", out_path, "-s", "zip"],
+            catch_exceptions=False,
+        )
+    assert result.exit_code == 0
+
+    import zipfile
+
+    with zipfile.ZipFile(out_path, "r") as zf:
+        zf.testzip()