From f559ced17d3019cc7915dfbba4ba4d72e80630c8 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Nov 2024 16:54:13 +0100
Subject: [PATCH 1/2] Prefer auto-decompressed datatype when picking conversion
 target

Fixes https://github.com/galaxyproject/galaxy/issues/18709
---
 lib/galaxy/datatypes/registry.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 671f30d82e16..a717dad0098f 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/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(

From 974d7e58bf56522175120c619e047cfd423374d2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 19 Nov 2024 17:21:45 +0100
Subject: [PATCH 2/2] Tighten conversion target input

This way we test that conversion to txt occurs via fasta, not the fasta
to tabular converter.
---
 test/functional/tools/implicit_conversion_format_input.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/functional/tools/implicit_conversion_format_input.xml b/test/functional/tools/implicit_conversion_format_input.xml
index e93f54095592..090aa474f0fc 100644
--- a/test/functional/tools/implicit_conversion_format_input.xml
+++ b/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" />