--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read2mut.xml	Sun Oct 04 17:19:39 2020 +0000
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.2" profile="19.01">
+    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
+    <macros>
+        <import>va_macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.1.0">xlsxwriter</requirement>
+    </expand>
+    <command><![CDATA[
+        ln -s '$file2' bam_input.bam &&
+        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
+        python '$__tool_directory__/read2mut.py' 
+        --mutFile '$file1'
+        --bamFile bam_input.bam
+        --inputJson '$file3'
+        --sscsJson '$file4'
+        --thresh '$thresh'
+        --phred '$phred'
+        --trim '$trim'
+        $chimera_correction
+        --outputFile '$output_xlsx'
+    ]]>
+    </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="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="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="Add additional tier for chimeric variants and correct the variant frequencies."/>
+    </inputs>
+    <outputs>
+        <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
+            <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/>
+            <param name="file3" value="tag_count_dict_test_data_VA.json"/>
+            <param name="file4" value="SSCS_counts_test_data_VA.json"/>
+            <param name="thresh" value="0"/>
+            <param name="phred" value="20"/>
+            <param name="trim" value="10"/>
+            <param name="chimera_correction" value="False"/>
+            <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.xlsx" decompress="true" lines_diff="10"/>
+        </test>
+    </tests>
+    <help> <![CDATA[
+**What it does**
+
+Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files 
+created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats** 
+as input and calculates frequencies and stats for DCS mutations based on information 
+from the raw reads.
+
+**Input** 
+
+**Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as 
+generated by the **Variant Annotator** tool.
+
+**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 
+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 
+is called in the DCS.
+
+**Output**
+
+The output is an XLSX file containing frequencies stats for DCS mutations based 
+on information from the raw reads. In addition to that a tier based 
+classification is provided based on the amout of support for a true variant call.
+
+    ]]> 
+    </help>
+    <expand macro="citation" />
+</tool>