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comparison mut2sscs.xml @ 78:fdfe9a919ff7 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author mheinzl
date Fri, 22 Jul 2022 09:19:44 +0000
parents 6ccff403db8a
children e46d5e377760
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77:1797e461d674 78:fdfe9a919ff7
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="2.1.1" profile="19.01"> 2 <tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="3.0.0" 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 carries 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 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command><![CDATA[ 8 <command><![CDATA[
13 --bamFile bam_input.bam 13 --bamFile bam_input.bam
14 --outputJson '$output_json' 14 --outputJson '$output_json'
15 ]]> 15 ]]>
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/> 18 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
19 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/> 19 <param name="file2" type="data" format="bam" label="SSCS BAM File" optional="false" help="BAM file with aligned SSCS reads."/>
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 22 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test> 25 <test>
26 <param name="file1" value="FreeBayes_test.vcf"/> 26 <param name="file1" value="FreeBayes_test.vcf"/>
27 <param name="file2" value="SSCS_test.bam"/> 27 <param name="file2" value="SSCS_test.bam"/>
28 <output name="output_json" file="SSCS_counts_test.json" lines_diff="2"/> 28 <output name="output_json" file="SSCS_counts_test.json"/>
29 </test> 29 </test>
30 </tests> 30 </tests>
31 <help> <![CDATA[ 31 <help> <![CDATA[
32 **What it does** 32 **What it does**
33 33
34 Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads 34 Takes a VCF file with DCS mutations and a BAM file of aligned SSCS reads
35 as input and writes statistics about tags of reads that carry a mutation in the 35 as input and writes statistics about tags of reads that carry a mutation and the reference allele in the
36 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.
37 37
38 **Input** 38 **Input**
39 39
40 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 40 **Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g.
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. 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.
42 42
43 **Dataset 2:** BAM file of aligned single stranded consensus sequence (SSCS) 43 **Dataset 2:** BAM file of the aligned single stranded consensus sequence (SSCS)
44 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
45 <https://arxiv.org/abs/1303.3997>`_. 45 <https://arxiv.org/abs/1303.3997>`_.
46 46
47 **Output** 47 **Output**
48 48
49 The output is a json file containing dictonaries with stats of tags that carry a mutation in the SSCS 49 The output is a json file containing dictionaries with stats of tags that carry a mutation in the SSCS
50 at the same position a mutation is called in the DCS. 50 at the same position, a mutation is called in the DCS.
51 51
52 ]]> 52 ]]>
53 </help> 53 </help>
54 <expand macro="citation" /> 54 <expand macro="citation" />
55 </tool> 55 </tool>