From 3fafbb5e34ed3f6f547bf1f184782b0f6967cf2f Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Tue, 15 Sep 2015 16:47:40 +0100
Subject: [PATCH 1/2] Fix more MissingToolException when running
 "./run_tests.sh -api" without "-with_framework_test_tools".

---
 test/api/test_workflow_extraction.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/api/test_workflow_extraction.py b/test/api/test_workflow_extraction.py
index 1307bc9f140..39cf87abba2 100644
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -142,6 +142,7 @@ test_data:
         collection_step_state = loads( collection_step[ "tool_state" ] )
         self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
 
+    @skip_without_tool( "cat_collection" )
     def test_subcollection_mapping( self ):
         jobs_summary = self._run_jobs("""
 steps:
@@ -180,6 +181,7 @@ test_data:
         collection_step_state = loads( collection_step[ "tool_state" ] )
         self.assertEquals( collection_step_state[ "collection_type" ], u"list:paired" )
 
+    @skip_without_tool( "collection_split_on_column" )
     def test_extract_workflow_with_output_collections( self ):
         jobs_summary = self._run_jobs("""
 steps:
@@ -223,6 +225,7 @@ test_data:
             tool_ids=tool_ids,
         )
 
+    @skip_without_tool( "collection_creates_pair" )
     def test_extract_with_mapped_output_collections( self ):
         jobs_summary = self._run_jobs("""
 steps:

From 63d1715679fb714f4c8f5ae426106edf6988e7ab Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
Date: Tue, 15 Sep 2015 17:06:27 +0100
Subject: [PATCH 2/2] Fix API tests using collection_creates_pair tool.

---
 lib/galaxy/tools/__init__.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 263437fe72f..8c9ab61ffd5 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -295,15 +295,17 @@ class ToolOutput( ToolOutputBase ):
 
 class ToolOutputCollection( ToolOutputBase ):
     """
-    Represents a HistoryDatasetCollectionAssociation of  output datasets produced by a tool.
+    Represents a HistoryDatasetCollectionAssociation of output datasets produced
+    by a tool.
+
     <outputs>
-      <dataset_collection type="list" label="${tool.name} on ${on_string} fasta">
+      <collection type="list" label="${tool.name} on ${on_string} fasta">
         <discover_datasets pattern="__name__" ext="fasta" visible="True" directory="outputFiles" />
-      </dataset_collection>
-      <dataset_collection type="paired" label="${tool.name} on ${on_string} paired reads">
+      </collection>
+      <collection type="paired" label="${tool.name} on ${on_string} paired reads">
         <data name="forward" format="fastqsanger" />
         <data name="reverse" format="fastqsanger"/>
-      </dataset_collection>
+      </collection>
     <outputs>
     """
 
@@ -337,13 +339,10 @@ class ToolOutputCollection( ToolOutputBase ):
         if self.dynamic_structure:
             return []
 
-        def to_part( ( element_identifier, output ) ):
-            return ToolOutputCollectionPart( self, element_identifier, output )
-
         # This line is probably not right - should verify structured_like
         # or have outputs and all outputs have name.
         if len( self.outputs ) > 1:
-            output_parts = map( to_part, self.outputs )
+            output_parts = [ToolOutputCollectionPart(self, k, v) for k, v in self.outputs.iteritems()]
         else:
             # either must have specified structured_like or something worse
             if self.structure.structured_like: