diff macros.xml @ 0:1d509fa3ec39 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d

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+++ b/macros.xml	Tue May 28 11:06:59 2024 +0000
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+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.7</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@unpublished{Fuchs2020,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>