From a42d7f30a74638a2d5baeaccbca17f0e480b67f9 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Fri, 29 Nov 2024 12:30:30 +0100
Subject: [PATCH 1/3] Create harmonized collections from correct tool outputs

---
 lib/galaxy/tools/__init__.py                  |  7 ++---
 .../tools/harmonize_two_collections_list.xml  | 31 +++++++++++++++++++
 2 files changed, 34 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 42fe49f58f4d..97fd83f8561a 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/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:
diff --git a/lib/galaxy/tools/harmonize_two_collections_list.xml b/lib/galaxy/tools/harmonize_two_collections_list.xml
index 7828ec5138e6..f580779835f1 100644
--- a/lib/galaxy/tools/harmonize_two_collections_list.xml
+++ b/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.fastq" 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.fastq" ftype="fastqsanger" />
+                    <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 

From 129b8a21254175a50259a320e5141b6e7ea535c7 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Fri, 29 Nov 2024 13:50:44 +0100
Subject: [PATCH 2/3] Fix test file type

---
 lib/galaxy/tools/harmonize_two_collections_list.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/harmonize_two_collections_list.xml b/lib/galaxy/tools/harmonize_two_collections_list.xml
index f580779835f1..546351802e77 100644
--- a/lib/galaxy/tools/harmonize_two_collections_list.xml
+++ b/lib/galaxy/tools/harmonize_two_collections_list.xml
@@ -182,7 +182,7 @@
                 <collection type="list:paired">
                     <element name="element_1">
                         <collection type="paired">
-                            <element name="forward" value="1.fastq" ftype="fastqsanger" />
+                            <element name="forward" value="1.fastq" ftype="fastq" />
                             <element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
                          </collection>
                     </element>
@@ -197,7 +197,7 @@
             </output_collection>
             <output_collection name="output2" type="list:paired" count="1">
                 <element name="element_1">
-                    <element name="forward" file="1.fastq" ftype="fastqsanger" />
+                    <element name="forward" file="1.fastq" ftype="fastq" />
                     <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
                 </element>
             </output_collection>

From 891d7aa0bfc8f70d0ece6e731687712b634a9bf5 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Fri, 29 Nov 2024 15:08:35 +0100
Subject: [PATCH 3/3] Try to fix tool test

---
 lib/galaxy/tools/harmonize_two_collections_list.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/harmonize_two_collections_list.xml b/lib/galaxy/tools/harmonize_two_collections_list.xml
index 546351802e77..3a12173f04e8 100644
--- a/lib/galaxy/tools/harmonize_two_collections_list.xml
+++ b/lib/galaxy/tools/harmonize_two_collections_list.xml
@@ -182,7 +182,7 @@
                 <collection type="list:paired">
                     <element name="element_1">
                         <collection type="paired">
-                            <element name="forward" value="1.fastq" ftype="fastq" />
+                            <element name="forward" value="1.fastqsanger" ftype="fastqsanger" />
                             <element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
                          </collection>
                     </element>
@@ -197,7 +197,7 @@
             </output_collection>
             <output_collection name="output2" type="list:paired" count="1">
                 <element name="element_1">
-                    <element name="forward" file="1.fastq" ftype="fastq" />
+                    <element name="forward" file="1.fastqsanger" ftype="fastqsanger" />
                     <element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
                 </element>
             </output_collection>