Merge pull request #19222 from wm75/fix-harmonize

[24.0] Create harmonized collections from correct tool outputs

Author: mvdbeek

lib/galaxy/tools/__init__.py

@@ -3660,14 +3660,13 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
         final_sorted_identifiers = [
             element.element_identifier for element in elements1 if element.element_identifier in old_elements2_dict
         ]
-        # Raise Exception if it is empty
         if len(final_sorted_identifiers) == 0:
             # Create empty collections:
             output_collections.create_collection(
-                next(iter(self.outputs.values())), "output1", elements={}, propagate_hda_tags=False
+                self.outputs["output1"], "output1", elements={}, propagate_hda_tags=False
             )
             output_collections.create_collection(
-                next(iter(self.outputs.values())), "output2", elements={}, propagate_hda_tags=False
+                self.outputs["output2"], "output2", elements={}, propagate_hda_tags=False
             )
             return
 
@@ -3685,7 +3684,7 @@ def output_with_selected_identifiers(old_elements_dict, output_label):
             self._add_datasets_to_history(history, new_elements.values())
             # Create collections:
             output_collections.create_collection(
-                next(iter(self.outputs.values())), output_label, elements=new_elements, propagate_hda_tags=False
+                self.outputs[output_label], output_label, elements=new_elements, propagate_hda_tags=False
             )
 
         # Create outputs:

lib/galaxy/tools/harmonize_two_collections_list.xml

@@ -171,6 +171,37 @@
             <output_collection name="output1" type="list" count="0"/>
             <output_collection name="output2" type="list" count="0"/>
         </test>
+        <!-- test that collection types get propagated to outputs correctly -->
+        <test>
+            <param name="input1">
+                <collection type="list">
+                    <element name="element_1" value="simple_line.txt" />
+                </collection>
+            </param>
+            <param name="input2">
+                <collection type="list:paired">
+                    <element name="element_1">
+                        <collection type="paired">
+                            <element name="forward" value="1.fastqsanger" ftype="fastqsanger" />
+                            <element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
+                         </collection>
+                    </element>
+                </collection>
+            </param>
+            <output_collection name="output1" type="list" count="1">
+                <element name="element_1">
+                    <assert_contents>
+                        <has_text_matching expression="^This is a line of text.\n$" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="output2" type="list:paired" count="1">
+                <element name="element_1">
+                    <element name="forward" file="1.fastqsanger" ftype="fastqsanger" />
+                    <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[