--- a/consensus.xml	Tue Sep 26 10:10:53 2023 +0000
+++ b/consensus.xml	Tue Oct 28 09:57:32 2025 +0000
@@ -1,5 +1,5 @@
-<tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
-    <description>Assembly polishing via neural networks</description>
+<tool id="medaka_consensus" name="medaka inference tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description> inference from a trained model and alignments.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -13,7 +13,7 @@
 ## Possibly new options bam_chunk and bam_workers. Should we be setting these?
 
 ## run
-medaka consensus
+medaka inference
 ## optional
 --debug ## increase log level
 --threads \${GALAXY_SLOTS:-4}
@@ -43,9 +43,7 @@
 $tag_keep_missing
 ## required
 alignment.bam ## bam
-'$out_result' ## output
-
-2>&1 | tee '$out_log'
+'$out_result'  2>&1 | tee log.txt
     ]]></command>
     <inputs>
         <param argument="bam" type="data" format="bam" label="Select input alignment"/>
@@ -84,7 +82,7 @@
             <filter>'result' in out</filter>
         </data>
         <!-- optional -->
-        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
+        <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>
@@ -94,14 +92,14 @@
             <param name="bam" value="alignment.bam"/>
             <output name="out_result">
                 <assert_contents>
-                    <has_size value="30960"/>
+                    <has_size value="26144"/>
                 </assert_contents>
             </output>
         </test>
         <!-- #2 -->
         <test expect_num_outputs="2">
             <param name="bam" value="alignment.bam"/>
-            <param name="model" value="r941_min_fast_g303"/>
+            <param name="model" value="r941_min_fast_g507"/>
             <param name="batch_size" value="99"/>
             <param name="chunk_len" value="9999"/>
             <param name="chunk_ovlp" value="999"/>
@@ -111,12 +109,12 @@
             <param name="out" value="result,log"/>
             <output name="out_result">
                 <assert_contents>
-                    <has_size value="37088"/>
+                    <has_size value="27104"/>
                 </assert_contents>
             </output>
             <output name="out_log">
                 <assert_contents>
-                    <has_text_matching expression=".+Validating and finalising output data."/>
+                    <has_text_matching expression=".+Running prediction at full precision"/>
                 </assert_contents>
             </output>
         </test>
@@ -150,4 +148,4 @@
 @REFERENCES@
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>