Implement optional collection params.

Was already parsing optional attribute but I put exactly zero thought into the implementation so these didn't work at all I don't think. This fills out the implementation, adds a test tool, and some cheetah helpers to facilitate this: "#if $collect_param" will fail if input not supplied or collection is empty and "#if $collect_param.is_input_supplied" will fail is input not supplied (i.e. empty collections will pass this check).

lib/galaxy/tools/actions/__init__.py

@@ -114,6 +114,8 @@ class DefaultToolAction( object ):
                         #allow explicit conversion to be stored in job_parameter table
                         target_dict[ conversion_name ] = conversion_data.id  # a more robust way to determine JSONable value is desired
             elif isinstance( input, DataCollectionToolParameter ):
+                if not value:
+                    return
                 for i, v in enumerate( value.collection.dataset_instances ):
                     data = v
                     current_user_roles = trans.get_current_user_roles()

lib/galaxy/tools/wrappers.py

@@ -269,6 +269,12 @@ class DatasetCollectionWrapper( object, HasDatasets ):
     def __init__( self, has_collection, dataset_paths=[], **kwargs ):
         super(DatasetCollectionWrapper, self).__init__()
 
+        if has_collection is None:
+            self.__input_supplied = False
+            return
+        else:
+            self.__input_supplied = True
+
         if hasattr( has_collection, "name" ):
             # It is a HistoryDatasetCollectionAssociation
             collection = has_collection.collection
@@ -298,20 +304,37 @@ class DatasetCollectionWrapper( object, HasDatasets ):
         self.element_instance_list = element_instance_list
 
     def keys( self ):
+        if not self.__input_supplied:
+            return []
         return self.element_instances.keys()
 
     @property
     def is_collection( self ):
         return True
 
+    @property
+    def is_input_supplied( self ):
+        return self.__input_supplied
+
     def __getitem__( self, key ):
+        if not self.__input_supplied:
+            return None
         if isinstance( key, int ):
             return self.element_instance_list[ key ]
         else:
             return self.element_instances[ key ]
 
     def __getattr__( self, key ):
+        if not self.__input_supplied:
+            return None
         return self.element_instances[ key ]
 
     def __iter__( self ):
+        if not self.__input_supplied:
+            return [].__iter__()
         return self.element_instance_list.__iter__()
+
+    def __nonzero__( self ):
+        # Fail `#if $param` checks in cheetah is optional input
+        # not specified or if resulting collection is empty.
+        return self.__input_supplied and bool( self.element_instance_list )

test/functional/tools/collection_optional_param.xml

@@ -0,0 +1,38 @@
+<tool id="collection_optional_param" name="collection_optional_param" version="0.1.0">
+  <command>
+    #if $f1
+      cat $f1.forward $f1['reverse'] >> $out1;
+    #else
+      echo "No input specified." >> $out1;
+    #end if
+  </command>
+  <inputs>
+    <param name="f1" type="data_collection" collection_type="paired" optional="true" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="out1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="f1">
+        <collection type="paired">
+          <element name="forward" value="simple_line.txt" />
+          <element name="reverse" value="simple_line_alternative.txt" />
+        </collection>
+      </param>
+      <output name="out1">
+        <assert_contents>
+          <has_line line="This is a line of text." />
+          <has_line line="This is a different line of text." />
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <output name="out1">
+        <assert_contents>
+          <has_line line="No input specified." />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -22,4 +22,5 @@
   <tool file="collection_nested_test.xml" />
   <tool file="collection_mixed_param.xml" />
   <tool file="collection_two_paired.xml" />
+  <tool file="collection_optional_param.xml" />
 </toolbox>