--- a/refchooser.xml	Mon Dec 08 20:28:57 2025 +0000
+++ b/refchooser.xml	Mon Mar 16 15:02:07 2026 +0000
@@ -1,7 +1,8 @@
-<tool id="refchooser" name="Refchooser" version="0.2.1" python_template_version="3.5" profile="21.05">
+<tool id="refchooser" name="Refchooser" version="0.2.1+galaxy0.1" python_template_version="3.5" profile="21.05">
     <description>Select centroidal assembly from a collection of closely-related assemblies, for reference purposes</description>
     <requirements>
-        <container type="docker">quay.io/galaxytrakr/refchooser:0.2.3</container>
+        <container type="docker">cfsanbiostatistics/refchooser:0.2.1</container>
+        
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./assemblies &&
@@ -13,16 +14,15 @@
         export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
         echo "*** best accession \$BEST ***" >&2 &&
         mkdir output &&
-        cp ./assemblies/\$BEST.fasta output/\$BEST.fasta &&
-        ls -l output/
+        cp ./assemblies/\$BEST.fasta output/\$BEST.fasta
     ]]></command>
     <inputs>
         <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
     </inputs>
     <outputs>
         <data name="matrix" label="Refchooser distance matrix for $on_string" format="tsv" hidden="false" />
-        <data name="best" format="txt" label="Centroidal_assembly" >
-            <discover_datasets directory="output" pattern="__designation_and_ext__" ext="fasta" assign_primary_output="true" visible="true" />
+        <data name="best" format="txt" label="Best assembly" visible="false" >
+            <discover_datasets directory="output" pattern="__designation_and_ext__" assign_primary_output="true" visible="true" />
         </data>
     </outputs>
     <tests>