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comparison mut2sscs.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="mut2sscs" name="DCS mutations to SSCS stats:" version="2.0.1" profile="19.01"> 2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="2.1.0" profile="19.01">
3 <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> 3 <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>
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 '$__tool_directory__/mut2sscs.py' 11 python '$__tool_directory__/mut2sscs.py'
17 --mutFile '$file1' 12 --mutFile '$file1'
41 SSCS at the same position a mutation is called in the DCS to a user specified output file.. 36 SSCS at the same position a mutation is called in the DCS to a user specified output file..
42 37
43 **Input** 38 **Input**
44 39
45 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 40 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
46 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. 41 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.
47 42
48 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS) 43 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS)
49 reads. This file can be obtained by the tool `Map with BWA-MEM 44 reads. This file can be obtained by the tool `Map with BWA-MEM
50 <https://arxiv.org/abs/1303.3997>`_. 45 <https://arxiv.org/abs/1303.3997>`_.
51 46