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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
author iuc
date Mon, 26 Aug 2024 18:10:11 +0000
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1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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1 <?xml version="1.0"?>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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2 <macros>
1
259e86ec88e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
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3 <token name="@TOOL_VERSION@">0.7.1</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">21.01</token>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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6 <xml name="biotools">
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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7 <xrefs>
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8 <xref type="bio.tools">virheat</xref>
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9 </xrefs>
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10 </xml>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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11 <xml name="requirements">
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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12 <requirements>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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13 <requirement type="package" version="@TOOL_VERSION@">virheat</requirement>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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14 <yield/>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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15 </requirements>
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16 </xml>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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17 <xml name="version">
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18 <version_command>virheat --version</version_command>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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19 </xml>
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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20 <token name="@HELP_HEADER@"><![CDATA[
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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21 What it does
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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22 ============
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23
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24 This tool generates multi-sample variant-frequency plots from SnpEff-annotated
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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25 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.
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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27 The tool expects either the length of a reference genome or the gff3 file if the sequence annotation is needed.
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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29 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.
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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31 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.
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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33 The tool expects input variant lists in VCF format. VCF datasets as produced by standard variant callers with
1d509fa3ec39 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
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34
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35 - variant allele frequencies encoded in an ``AF`` INFO field
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36 - variant functional genomic effects annotated using SnpEff's EFF format
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37
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38 ]]></token>
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39 <xml name="citations">
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40 <citations>
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41 <citation type="bibtex">@unpublished{Fuchs2020,
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42 author = {Fuchs, Jonas},
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43 title = {},
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44 year = {2020},
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45 note = {Multi-sample annotated viral variant-frequency plots based on the R pheatmap package.},
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46 address = {Institute for Virology, University of Freiburg}
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47 }</citation>
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48 </citations>
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49 </xml>
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50 </macros>