diff mut2read.xml @ 72:3691922baa08 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/mut2read.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/mut2read.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,15 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01">
+<tool id="mut2read" name="DCS mutations to tags/reads:" version="2.1.0" profile="19.01">
     <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
     <macros>
         <import>va_macros.xml</import>
     </macros>
-	<requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="1.4.0">matplotlib</requirement>
-        <requirement type="package" version="0.15">pysam</requirement>
-        <requirement type="package" version="0.11.6">cyvcf2</requirement>
-    </requirements>
+    <expand macro="requirements"/>
     <command><![CDATA[
         ln -s '$file2' bam_input.bam &&
         ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
@@ -50,7 +45,8 @@
 **Input** 
 
 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 
-generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
+generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
+
 
 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the 
 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.