--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mut2sscs.xml	Sun Oct 04 17:19:39 2020 +0000
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.1" 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>
+    <macros>
+        <import>va_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        ln -s '$file2' bam_input.bam &&
+        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
+        python '$__tool_directory__/mut2sscs.py' 
+        --mutFile '$file1'
+        --bamFile bam_input.bam
+        --outputJson '$output_json'
+    ]]>
+    </command>
+    <inputs>
+        <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
+        <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
+    </inputs>
+    <outputs>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
+    </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"/>
+        </test>
+    </tests>
+    <help> <![CDATA[
+**What it does**
+
+Takes a tabular 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 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 
+at the same position a mutation is called in the DCS.
+
+    ]]> 
+    </help>
+    <expand macro="citation" />
+</tool>