Merge pull request #1502 from jmchilton/planemo_fix

[16.01] Fix a few problems discovered through planemo.

lib/galaxy/tools/cwl/cwltool_deps.py

@@ -23,10 +23,9 @@ try:
 except ImportError:
     shellescape = None
 
-if job is not None:
-    needs_shell_quoting = job.needs_shell_quoting
-else:
-    needs_shell_quoting = None
+import re
+
+needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
 
 
 def ensure_cwltool_available():

lib/galaxy/tools/deps/resolvers/__init__.py

@@ -27,11 +27,11 @@ class DependencyResolver(Dictifiable, object):
         version for instance if the request version is 'default'.)
         """
 
-    def _get_config_option(self, key, dependency_resolver, default=None, prefix=None, **kwds):
+    def _get_config_option(self, key, dependency_resolver, default=None, config_prefix=None, **kwds):
         """ Look in resolver-specific settings for option and then fallback to
         global settings.
         """
-        global_key = "%s_%s" % (prefix, key)
+        global_key = "%s_%s" % (config_prefix, key)
         if key in kwds:
             return kwds.get(key)
         elif global_key in dependency_resolver.extra_config:

lib/galaxy/tools/deps/resolvers/conda.py

@@ -42,7 +42,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
 
         def get_option(name):
-            return self._get_config_option(name, dependency_manager, prefix="conda", **kwds)
+            return self._get_config_option(name, dependency_manager, config_prefix="conda", **kwds)
 
         # Conda context options (these define the environment)
         conda_prefix = get_option("prefix")