diff mut2sscs.xml @ 72:3691922baa08 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Fri, 19 Mar 2021 14:05:39 +0000
parents d21960b45a6b
children 6ccff403db8a
line wrap: on
line diff
--- a/mut2sscs.xml	Fri Mar 19 13:54:14 2021 +0000
+++ b/mut2sscs.xml	Fri Mar 19 14:05:39 2021 +0000
@@ -1,15 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" profile="19.01">
+<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.1.0" profile="19.01">
     <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</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 &&
@@ -43,7 +38,7 @@
 **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 single stranded consensus sequence (SSCS) 
 reads. This file can be obtained by the tool `Map with BWA-MEM