--- a/variant.xml	Tue Sep 26 10:11:35 2023 +0000
+++ b/variant.xml	Tue Oct 28 09:58:30 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="medaka_variant" name="medaka vcf tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>decodes variant calls from medaka consensus output</description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
 
 #if $pool.pool_mode == "Yes":
     ## run
-    medaka variant
+    medaka vcf
     ## optional
     --debug
     #if $regions
@@ -22,13 +22,13 @@
     ${ambig_ref}
     ${gvcf}
     ## required
-    reference.fa
     #for $current in $pool.inputs
         '$current'
     #end for
+    reference.fa
 #elif $pool.pool_mode == "No":
     ## run
-    medaka variant
+    medaka vcf
     ## optional
     --debug
     #if $regions
@@ -38,15 +38,13 @@
     ${ambig_ref}
     ${gvcf}
     ## required
+    '$pool.input'
     reference.fa
-    '$pool.input'
 #end if
 #if str($output_annotated.output_annotated_select) == 'false':
-    '$out_variants' ##output
-    2>&1 | tee '$out_log'
+    '$out_variants' 2>&1 | tee log.txt
 #else
-    raw.vcf ##output of medaka variant
-    2>&1 | tee '$out_log'
+    raw.vcf 2>&1 | tee log.txt
     && ln -s '$output_annotated.in_bam' in.bam
     && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
     && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
@@ -98,7 +96,7 @@
     </inputs>
     <outputs>
         <data name="out_variants" format="vcf" label="${tool.name} on ${on_string}: called variants"/>
-        <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
+        <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
             <filter>output_log_bool</filter>
         </data>
     </outputs>