Improved integration testing for test command.

tests/data/tools/bwa_wrong_version.xml

@@ -0,0 +1,28 @@
+<tool id="bwa" name="BWA" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="0.7.12">bwa</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="2:" />
+    </stdio>
+    <command><![CDATA[
+        bwa > $output_1 2>&1
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+      <data name="output_1" />
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <tests>
+      <test>
+        <output name="output_1">
+          <assert_contents>
+            <has_text text="Version: 0.7.10" />
+          </assert_contents>
+        </output>
+      </test>
+    </tests>
+</tool>

tests/test_cmd_test.py

@@ -17,7 +17,6 @@ class CmdTestTestCase(CliTestCase):
     """Integration tests for the ``test`` command."""
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
     @skip_unless_environ("PLANEMO_RUN_BETA_TESTS")
     def test_workflow_test_simple(self):
         """Test testing a simple workflow with Galaxy."""

tests/test_cmd_test_conda.py

@@ -0,0 +1,43 @@
+"""Module contains :class:`CmdTestTestCase` - integration tests for the ``test`` command."""
+import os
+
+from .test_utils import (
+    CliTestCase,
+    PROJECT_TEMPLATES_DIR,
+    skip_if_environ,
+    TEST_TOOLS_DIR,
+)
+
+
+class CmdTestTestCase(CliTestCase):
+    """Integration tests for the ``test`` command."""
+
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_conda_dependencies(self):
+        with self._isolate():
+            bwa_test = os.path.join(PROJECT_TEMPLATES_DIR, "conda_testing", "bwa.xml")
+            test_command = [
+                "--verbose",
+                "test",
+                "--conda_dependency_resolution",
+                "--conda_auto_install",
+                "--conda_auto_init",
+                bwa_test,
+            ]
+            self._check_exit_code(test_command, exit_code=0)
+
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_conda_dependencies_version(self):
+        """Test testing a simple workflow with Galaxy."""
+        with self._isolate():
+            # Try a failing test to ensure the primary test above isn't just passing spuriously.
+            bwa_test = os.path.join(TEST_TOOLS_DIR, "bwa_wrong_version.xml")
+            test_command = [
+                "--verbose",
+                "test",
+                "--conda_dependency_resolution",
+                "--conda_auto_install",
+                "--conda_auto_init",
+                bwa_test,
+            ]
+            self._check_exit_code(test_command, exit_code=1)