<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.7.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">virheat</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">virheat</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="version">
        <version_command>virheat --version</version_command>
    </xml>
    <token name="@HELP_HEADER@"><![CDATA[
What it does
============

This tool generates multi-sample variant-frequency plots from SnpEff-annotated
viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. 

The tool expects either the length of a reference genome or the gff3 file if the sequence annotation is needed.

Additionally, to analyze whether mutations are sufficiently covered and to display non-covered cells in grey, first create per-base coverage TSV files for each BAM file with Qualimap and provide them in the same folder as the VCF files. Give them the same name as your VCF files.

Moreover, there is an option to include visualizations of additional scores (e.g., MAVE scores for binding affinity, expression level, antibody escape, etc.) mapped to mutations on the heatmap.

The tool expects input variant lists in VCF format. VCF datasets as produced by standard variant callers with

   - variant allele frequencies encoded in an ``AF`` INFO field
   - variant functional genomic effects annotated using SnpEff's EFF format

]]></token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@unpublished{Fuchs2020,
                author = {Fuchs, Jonas},
                title = {},
                year = {2020},
                note = {Multi-sample annotated viral variant-frequency plots based on the R pheatmap package.},
                address = {Institute for Virology, University of Freiburg}
            }</citation>
        </citations>
    </xml>
</macros>