From 0611465e3bbea77db56c4738e87a4db39717dc85 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 9 Apr 2024 11:36:10 +0100
Subject: [PATCH] Fix output datatype when uncompressing a dataset with
 incorrect datatype

with the ``CONVERTER_gz_to_uncompressed`` tool.

Previously, if a user forced an incorrect datatype to a compressed input
dataset (e.g. `fastqsanger` instead of `fastqsanger.gz`), then the output
datatype assigned by this tool would be an invalid one (`fastqsan`).

Fix #17938.
---
 .../datatypes/converters/gz_to_uncompressed.xml       | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/gz_to_uncompressed.xml b/lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
index af1ab71f6d29..4ff4b8344fa4 100644
--- a/lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
+++ b/lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
@@ -6,7 +6,7 @@ gzip -dcf '$input1' > '$output1'
     <configfiles>
         <configfile name="ext_config">{"output1": {
   "name": "${input1.name[0:-len('.gz')] if $input1.name.endswith('.gz') else $input1.name} uncompressed",
-  "ext": "${input1.ext[0:-len('.gz')] if $input1.ext != 'vcf_bgzip' else 'vcf'}"
+  "ext": "${'vcf' if $input1.ext == 'vcf_bgzip' else $input1.ext[0:-len('.gz')] if $input1.ext.endswith('.gz') else $input1.ext}"
 }}</configfile>
     </configfiles>
     <inputs>
@@ -21,6 +21,15 @@ gzip -dcf '$input1' > '$output1'
             <param name="input1" value="test.vcf.gz" ftype="vcf_bgzip"/>
             <output name="output1" file="test.vcf" ftype="vcf"/>
         </test>
+        <test>
+            <param name="input1" value="1.fasta.gz" ftype="fasta.gz"/>
+            <output name="output1" file="1.fasta" ftype="fasta"/>
+        </test>
+        <!-- Test input with wrong format -->
+        <test>
+            <param name="input1" value="1.fasta.gz" ftype="fasta"/>
+            <output name="output1" file="1.fasta" ftype="fasta"/>
+        </test>
     </tests>
     <help>
     </help>