--- a/read2mut.xml	Mon Mar 29 09:22:57 2021 +0000
+++ b/read2mut.xml	Fri Jul 22 09:19:44 2022 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.4" profile="19.01">
-    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
+<tool id="read2mut" name="Call specific mutations in reads:" version="3.0.0" 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>
     </macros>
@@ -28,12 +28,12 @@
     ]]>
     </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="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
         <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/>
         <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
-        <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
-        <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
+        <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occurring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
+        <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold is considered. Default = 20."/>
         <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 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"/>
@@ -57,10 +57,10 @@
             <param name="chimera_correction"/>
             <param name="softclipping_dist" value="15"/>
             <param name="reads_threshold" value="1.0"/>
-            <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
-            <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
-            <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
-            <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
+            <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"/>
+            <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true"/>
         </test>
     </tests>
     <help> <![CDATA[
@@ -73,25 +73,25 @@
 
 **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 raw reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
 
 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool 
-containing dictonaries of the tags of reads containing mutations 
+containing dictionaries of the tags of reads containing mutations 
 in the DCS.
 
 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool 
-stats of tags that carry a mutation in the SSCS at the same position a mutation 
+stats of tags that carry a mutation and the reference allele in the SSCS at the same position a mutation 
 is called in the DCS.
 
 **Output**
 
-The output are three XLSX files containing frequencies stats for DCS mutations based 
-on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based 
-classification is provided based on the amout of support for a true variant call.
+The output is three XLSX files containing frequencies stats for DCS mutations based 
+on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that, a tier-based 
+classification is provided based on the amount of support for a true variant call.
 
 
     ]]>