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comparison mut2read.xml @ 72:3691922baa08 draft

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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
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71:8664c0aa91c3 72:3691922baa08
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01"> 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.1.0" profile="19.01">
3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> 3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
4 <macros> 4 <macros>
5 <import>va_macros.xml</import> 5 <import>va_macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <expand macro="requirements"/>
8 <requirement type="package" version="2.7">python</requirement>
9 <requirement type="package" version="1.4.0">matplotlib</requirement>
10 <requirement type="package" version="0.15">pysam</requirement>
11 <requirement type="package" version="0.11.6">cyvcf2</requirement>
12 </requirements>
13 <command><![CDATA[ 8 <command><![CDATA[
14 ln -s '$file2' bam_input.bam && 9 ln -s '$file2' bam_input.bam &&
15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && 10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
16 python '$__tool_directory__/mut2read.py' 11 python '$__tool_directory__/mut2read.py'
17 --mutFile '$file1' 12 --mutFile '$file1'
48 reads of tags with a mutation. 43 reads of tags with a mutation.
49 44
50 **Input** 45 **Input**
51 46
52 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 47 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
53 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. 48 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
49
54 50
55 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the 51 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the
56 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. 52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
57 53
58 **Dataset 3:** Tabular file with reads as produced by the 54 **Dataset 3:** Tabular file with reads as produced by the