--- a/nanopolish_variants.xml	Fri Jul 30 06:29:50 2021 +0000
+++ b/nanopolish_variants.xml	Thu Nov 30 17:57:59 2023 +0000
@@ -1,43 +1,11 @@
-<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0">
+<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_merged' reads.fasta && 
-        
-        #if $input_reads_raw.extension == 'fast5':
-            mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar':
-            ln -s '$input_reads_raw' fast5_files.tar &&
-            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
-            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
-            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
-
-        #else:
-            ln -s '$input_reads_raw' fast5_files.tar.gz &&
-            mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
-
-        #end if
-
-        nanopolish index 
-        -d fast5_files/
-        #if $adv.input_seq_summary:
-          -s '$adv.input_seq_summary'
-        #end if 
-        reads.fasta &&
-        
-        ln -s '$b' reads.bam &&
-        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
-        #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' genome.fa &&
-        #else:
-            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
-        #end if
+        @PREPROCESS_INPUTS@
         
         nanopolish variants
         -r reads.fasta
@@ -89,11 +57,11 @@
           --models-fofn '$input_models_fofn'
         #end if
 
-        && 
-
-        nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa
-
-
+        &&
+        nanopolish vcf2fasta
+            --skip-checks
+            -g genome.fa
+            variants.vcf > polished.fa
     ]]></command>
     <inputs>
       <!-- index inputs -->
@@ -131,7 +99,6 @@
        </section>
 
         <!-- optional params -->
-        <!-- optional params -->
         <param argument="-w" type="text" optional="true"
             label="find variants in window of region chromsome:start-end" />
         <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
@@ -251,8 +218,7 @@
     <help><![CDATA[
 
         Build an index mapping from basecalled reads to the signals measured by the sequencer
-        and
-        Find SNPs using a signal-level HMM
+        and find SNPs using a signal-level HMM.
 
         Tutorial and manual available at:
         http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html