Merge pull request #19162 from mvdbeek/optimize_converter_order

[24.1] Prefer auto-decompressed datatype when picking conversion target

lib/galaxy/datatypes/registry.py

@@ -881,7 +881,16 @@ def find_conversion_destination_for_dataset_by_extensions(
         if datatype and datatype.matches_any(accepted_datatypes):
             return True, None, None
 
-        for convert_ext in self.get_converters_by_datatype(ext):
+        converter_extensions = self.get_converters_by_datatype(ext)
+        uncompressed_instance = getattr(datatype, "uncompressed_datatype_instance", None)
+        if uncompressed_instance and uncompressed_instance.file_ext in converter_extensions:
+            # sort uncompressed instance ahead of other possible conversions
+            converter_extensions = [
+                uncompressed_instance.file_ext,
+                *(ext for ext in converter_extensions if ext != uncompressed_instance.file_ext),
+            ]
+
+        for convert_ext in converter_extensions:
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
                 self.log.warning(

test/functional/tools/implicit_conversion_format_input.xml

@@ -3,7 +3,7 @@
     cut -f 1 '$input1' > '$output1'
   </command>
   <inputs>
-    <param type="data" format="fasta" name="input1" label="Input 1" />
+    <param type="data" format="txt" name="input1" label="Input 1" />
   </inputs>
   <outputs>
     <data name="output1" format="input" />