--- a/consensus.xml	Mon Mar 29 20:06:22 2021 +0000
+++ b/consensus.xml	Thu Apr 22 20:24:25 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="medaka_consensus" name="medaka consensus tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -10,6 +10,8 @@
 ln -s '${bam}' alignment.bam &&
 ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&
 
+## Possibly new options bam_chunk and bam_workers. Should we be setting these?
+
 ## run
 medaka consensus
 ## optional
@@ -27,7 +29,6 @@
 --chunk_len $chunk_len
 --chunk_ovlp $chunk_ovlp
 --model $model
-$disable_cudnn
 $check_output
 $save_features
 #if $RG
@@ -66,7 +67,6 @@
         </conditional>
         <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
         <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
-        <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/>
         <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>
         <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/>
         <param argument="--RG" type="text" value="" optional="true" label="Set read group"/>
@@ -105,7 +105,6 @@
             <param name="batch_size" value="99"/>
             <param name="chunk_len" value="9999"/>
             <param name="chunk_ovlp" value="999"/>
-            <param name="disable_cudnn" value="true"/>
             <param name="check_output" value="true"/>
             <param name="save_features" value="true"/>
             <param name="tag_keep_missing" value="true"/>