 +genrule(
 +    name="gen_dir",
 +    outs=["someDir"],
-+    cmd="mkdir -p $@",
++    cmd="mkdir -p $@ && touch $@/foo.py",
 +)
 +
  # Package just a specific py_libraries, without their dependencies

+    deps = [
+        ":example_pkg_with_data"
+    ]
+)
+
 py_test(
     name = "wheel_test",
     srcs = ["wheel_test.py"],
diff --git experimental/tools/wheelmaker.py experimental/tools/wheelmaker.py
index 38fb122..4c7be30 100644
--- experimental/tools/wheelmaker.py
+++ experimental/tools/wheelmaker.py
@@ -102,6 +102,11 @@ class WheelMaker(object):

             return normalized_arcname

+        # If anywhere in the dependency tree a directory is set
+        # it will be passed in as an input file and we need to
+        # ignore.
+        if os.path.isdir(real_filename):
+            return
         arcname = arcname_from(package_filename)

         self._zipfile.write(real_filename, arcname=arcname)

diff --git experimental/examples/wheel/BUILD experimental/examples/wheel/BUILD
index d721e4c..065c775 100644
--- experimental/examples/wheel/BUILD
+++ experimental/examples/wheel/BUILD
@@ -31,6 +31,20 @@ py_library(
