--- a/mut2sscs.xml	Mon Mar 29 09:22:57 2021 +0000
+++ b/mut2sscs.xml	Fri Jul 22 09:19:44 2022 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.1.1" profile="19.01">
-    <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
+<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="3.0.0" profile="19.01">
+    <description>Extracts all tags from the single-stranded consensus sequence (SSCS) bam file that carries a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
@@ -15,7 +15,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
+        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
         <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
     </inputs>
     <outputs>
@@ -25,29 +25,29 @@
         <test>
             <param name="file1" value="FreeBayes_test.vcf"/>
             <param name="file2" value="SSCS_test.bam"/>
-            <output name="output_json" file="SSCS_counts_test.json" lines_diff="2"/>
+            <output name="output_json" file="SSCS_counts_test.json"/>
         </test>
     </tests>
     <help> <![CDATA[
 **What it does**
 
 Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads 
-as input and writes statistics about tags of reads that carry a mutation in the 
-SSCS at the same position a mutation is called in the DCS to a user specified output file..
+as input and writes statistics about tags of reads that carry a mutation and the reference allele in the 
+SSCS at the same position a mutation is called in the DCS to a user-specified output file.
 
 **Input** 
 
-**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
+**Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g. 
 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
 
-**Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS) 
+**Dataset 2:** BAM file of the aligned single stranded consensus sequence (SSCS) 
 reads. This file can be obtained by the tool `Map with BWA-MEM 
 <https://arxiv.org/abs/1303.3997>`_.
 
 **Output**
 
-The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS 
-at the same position a mutation is called in the DCS.
+The output is a json file containing dictionaries with stats of tags that carry a mutation in the SSCS 
+at the same position, a mutation is called in the DCS.
 
     ]]> 
     </help>