fix missing element_identifier with data_collection input parama

lib/galaxy/tools/wrappers.py

@@ -307,7 +307,7 @@ class DatasetListWrapper( list, ToolParameterValueWrapper, HasDatasets ):
                 element = dataset
                 dataset = element.dataset_instance
                 kwargs["identifier"] = element.element_identifier
-            return self._dataset_wrapper( dataset, dataset_paths, **kwargs )
+            return self._dataset_wrapper( dataset, dataset_paths, identifier = element_identifier, **kwargs )
 
         list.__init__( self, map( to_wrapper, datasets ) )
         self.job_working_directory = job_working_directory
@@ -365,7 +365,7 @@ class DatasetCollectionWrapper( ToolParameterValueWrapper, HasDatasets ):
             if dataset_collection_element.is_collection:
                 element_wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection_element, dataset_paths, **kwargs )
             else:
-                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, **kwargs)
+                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, identifier=element_identifier, **kwargs)
 
             element_instances[element_identifier] = element_wrapper
             element_instance_list.append( element_wrapper )

test/api/test_tools.py

@@ -806,8 +806,8 @@ class ToolsTestCase( api.ApiTestCase ):
         output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
         self.assertEquals( output1_content.strip(), "Pasted Entry\nPasted Entry" )
 
-    @skip_without_tool( "identifier_multiple_in_conditional" )
-    def test_identifier_with_multiple_normal_datasets_in_conditional( self ):
+    @skip_without_tool( "identifier_collection" )
+    def test_identifier_with_data_collection( self ):
         history_id = self.dataset_populator.new_history()
 
         element_identifiers = self.dataset_collection_populator.list_identifiers( history_id )
@@ -823,12 +823,11 @@ class ToolsTestCase( api.ApiTestCase ):
         dataset_collection = create_response.json()
 
         inputs = {
-            "options|choice": "one",
-            "options|input1": {'src': 'hdca', 'id': dataset_collection['id']},
+            "input1": {'src': 'hdca', 'id': dataset_collection['id']},
         }
 
         self.dataset_populator.wait_for_history( history_id, assert_ok=True )
-        create_response = self._run( "identifier_multiple_in_conditional", history_id, inputs )
+        create_response = self._run( "identifier_conditional", history_id, inputs )
         self._assert_status_code_is( create_response, 200 )
         create = create_response.json()
         outputs = create[ 'outputs' ]

test/functional/tools/identifier_conditional.xml

@@ -0,0 +1,15 @@
+<tool id="identifier_conditional" name="identifier_conditional">
+  <command>
+    #for $input in $input1:
+      echo '$input.element_identifier' >> 'output1';
+    #end for
+  </command>
+  <inputs>
+    <param type="data_collection" collection_type="list" name="input1" label="Input 1" multiple="true" />
+  </inputs>
+  <outputs>
+    <data name="output1" type="tabular" from_work_dir="output1" />
+  </outputs>
+  <tests>
+  </tests>
+</tool>

test/functional/tools/identifier_multiple_in_conditional.xml

@@ -1,28 +0,0 @@
-<tool id="identifier_multiple_in_conditional" name="identifier_multiple_in_conditional">
-  <command>
-    #if $options.choice == "one":
-        #for $input in $options.input1:
-          echo '$input.element_identifier' >> 'output1';
-        #end for
-    #end if
-  </command>
-  <inputs>
-    <conditional name="options">
-        <param name="choice" type="select" label="choice1">
-            <option value="one" selected="true">One</option>
-            <option value="two">Two</option>
-        </param>
-        <when value="one">
-            <param type="data_collection" collection_type="list" name="input1" label="Input 1" multiple="true" />
-        </when>
-        <when value="two">
-            <param type="data_collection" collection_type="list" name="input2" label="Input 2" multiple="true" />
-        </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data name="output1" type="tabular" from_work_dir="output1" />
-  </outputs>
-  <tests>
-  </tests>
-</tool>

test/functional/tools/samples_tool_conf.xml

@@ -64,7 +64,7 @@
   <tool file="validation_empty_dataset.xml" />
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
-  <tool file="identifier_multiple_in_conditional.xml" />
+  <tool file="identifier_conditional.xml" />
   <tool file="tool_directory.xml" />
   <tool file="output_action_change_format.xml" />
   <tool file="collection_paired_test.xml" />