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author mheinzl
date Sun, 04 Oct 2020 17:19:39 +0000
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<?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>
    <expand macro="requirements">
        <requirement type="package" version="1.1.0">xlsxwriter</requirement>
        ln -s '$file2' bam_input.bam &&
        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/' 
        --mutFile '$file1'
        --bamFile bam_input.bam
        --inputJson '$file3'
        --sscsJson '$file4'
        --thresh '$thresh'
        --phred '$phred'
        --trim '$trim'
        --outputFile '$output_xlsx'
        <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."/>
        <data name="output_xlsx" format="xlsx" label="${} on ${on_string}: XLSX"/>
            <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"/>
    <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.


**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 <>`_.

**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.


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.

    <expand macro="citation" />