--- a/refchooser.xml	Mon Aug 11 15:37:26 2025 +0000
+++ b/refchooser.xml	Mon Dec 08 20:28:57 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="refchooser" name="Refchooser" version="0.2.1" 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">cfsanbiostatistics/refchooser:0.2.1</container>
+        <container type="docker">quay.io/galaxytrakr/refchooser:0.2.3</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./assemblies &&
@@ -12,14 +12,18 @@
         refchooser matrix ./assemblies ./sketches ${matrix} &&
         export BEST=\$(refchooser metrics --sort Mean_Distance --top 1 ./assemblies ./sketches | tail -n 1 | cut -f 1) &&
         echo "*** best accession \$BEST ***" >&2 &&
-        cat ./assemblies/\$BEST.fasta > $output
+        mkdir output &&
+        cp ./assemblies/\$BEST.fasta output/\$BEST.fasta &&
+        ls -l output/
     ]]></command>
     <inputs>
         <param type="data_collection" collection_type="list" name="assemblies" format="fasta" />
     </inputs>
     <outputs>
-        <data name="matrix" label="Distance matrix" format="tsv" visible="false" />
-        <data name="output" label="Centroidal assembly" format="fasta" />
+        <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>
     </outputs>
     <tests>
         <test>
@@ -37,7 +41,13 @@
                     <element name="SRR498387" value="test/reference_selection/assemblies/SRR498387_contigs.fasta" />
                 </collection>
             </param>
-            <output name="output" value="test/reference_selection/assemblies/SRR498286_contigs.fasta" />
+            <output name="best" >
+                <discovered_dataset designation="SRR498286" ftype="fasta">
+                    <assert_contents>
+                        <has_text text="SRR498286" />
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
         </test>
     </tests>
     <help><![CDATA[