--- a/read2mut.xml	Fri Aug 05 08:23:34 2022 +0000
+++ b/read2mut.xml	Fri Aug 19 11:23:37 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="3.0.0" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="3.1.0" profile="19.01">
     <description>Looks for reads with a mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
@@ -19,6 +19,7 @@
         --phred '$phred'
         --trim '$trim'
         $chimera_correction
+        $refalttiers
         --softclipping_dist '$softclipping_dist'
         --reads_threshold '$reads_threshold'
         --outputFile '$output_xlsx'
@@ -37,7 +38,8 @@
         <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/>
         <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants (not for the reference allele) and correct the variant frequencies."/>
         <param name="softclipping_dist" type="integer" label="Distance between artifact and softclipping of the reads" min="1" value="15" help="Count mutation as an artifact if mutation lies within this parameter away from the softclipping part of the reads. Default = 20"/>
-<param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/>
+        <param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/>
+        <param name="refalttiers" type="boolean" label="Extract tiers also for reference allele" truevalue="--refalttiers" falsevalue="" checked="False" help="Extracts tier information for the alternate and reference allele. Note that this will increase the running time of the tool. Otherwise only the tier information for the alternate allele is extracted."/>
     </inputs>
     <outputs>
         <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
@@ -57,6 +59,7 @@
             <param name="chimera_correction"/>
             <param name="softclipping_dist" value="15"/>
             <param name="reads_threshold" value="1.0"/>
+            <param name="refalttiers"/>
             <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true"/>
             <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true"/>
             <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true"/>
@@ -84,7 +87,7 @@
 in the DCS.
 
 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool 
-stats of tags that carry a mutation and the reference allele in the SSCS at the same position a mutation 
+stats of tags that carry a mutation (and optional the reference allele) in the SSCS at the same position a mutation 
 is called in the DCS.
 
 **Output**