--- a/mut2sscs.xml	Tue Oct 27 12:46:55 2020 +0000
+++ b/mut2sscs.xml	Mon Jan 18 09:49:15 2021 +0000
@@ -1,10 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.1" profile="19.01">
+<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.0" 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>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="1.4.0">matplotlib</requirement>
+        <requirement type="package" version="0.15">pysam</requirement>
+        <requirement type="package" version="0.11.6">cyvcf2</requirement>
+    </requirements>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -15,7 +20,7 @@
     ]]>
     </command>
     <inputs>
-        <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR 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 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>
@@ -23,31 +28,27 @@
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
-            <param name="file2" value="SSCS_test_data_VA.bam"/>
-            <output name="output_json" file="SSCS_counts_test_data_VA.json" lines_diff="2"/>
+            <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"/>
         </test>
     </tests>
     <help> <![CDATA[
 **What it does**
 
-Takes a tabular file with DCS mutations and a BAM file of aligned SSCS reads 
+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..
 
 **Input** 
 
-**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 
-generated by the **Variant Annotator** tool.
+**Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
+generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
 
 **Dataset 2:** BAM file of 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>`_.
 
-**Dataset 3:** Tabular file with reads as produced by the 
-**Du Novo: Align families** tool of the `Du Novo Analysis Pipeline 
-<https://doi.org/10.1186/s13059-016-1039-4>`_
-
 **Output**
 
 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS