--- a/mut2read.xml	Mon Mar 29 09:22:57 2021 +0000
+++ b/mut2read.xml	Fri Jul 22 09:19:44 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.1.1" profile="19.01">
+<tool id="mut2read" name="DCS mutations to tags/reads:" version="3.0.0" profile="19.01">
     <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
     <macros>
         <import>va_macros.xml</import>
@@ -17,7 +17,7 @@
     ]]>
     </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="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
         <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
     </inputs>
@@ -27,11 +27,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/>
+            <param name="file1" value="FreeBayes_test.vcf"/>
             <param name="file2" value="DCS_test.bam"/>
             <param name="file3" value="Aligned_Families_test.tabular"/>
-            <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/>
-            <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
+            <output name="output_fastq" file="Interesting_Reads_test.fastq"/>
+            <output name="output_json" file="tag_count_dict_test.json"/>
         </test>
     </tests>
     <help> <![CDATA[
@@ -39,12 +39,12 @@
 
 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 
 tabular file with aligned families as input and prints all tags of reads that 
-carry a mutation to a user specified output file and creates a fastq file of 
-reads of tags with a mutation.
+carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of 
+reads of tags with a mutation and the reference allele.
 
 **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.
 
 
@@ -57,7 +57,7 @@
 
 **Output**
 
-The output is a json file containing dictonaries of the tags of reads containing mutations 
+The output is a json file containing dictionaries of the tags of reads containing mutations 
 in the DCS and a fastq file of all reads of these tags.
 
     ]]>