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comparison mut2read.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="mut2read" name="DCS mutations to tags/reads:" version="2.1.1" profile="19.01"> 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="3.0.0" 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 <expand macro="requirements"/> 7 <expand macro="requirements"/>
15 --outputFastq '$output_fastq' 15 --outputFastq '$output_fastq'
16 --outputJson '$output_json' 16 --outputJson '$output_json'
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <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."/> 20 <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."/>
21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> 21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> 22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
23 </inputs> 23 </inputs>
24 <outputs> 24 <outputs>
25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> 25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test> 29 <test>
30 <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/> 30 <param name="file1" value="FreeBayes_test.vcf"/>
31 <param name="file2" value="DCS_test.bam"/> 31 <param name="file2" value="DCS_test.bam"/>
32 <param name="file3" value="Aligned_Families_test.tabular"/> 32 <param name="file3" value="Aligned_Families_test.tabular"/>
33 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/> 33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/>
34 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/> 34 <output name="output_json" file="tag_count_dict_test.json"/>
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help> <![CDATA[ 37 <help> <![CDATA[
38 **What it does** 38 **What it does**
39 39
40 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 40 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a
41 tabular file with aligned families as input and prints all tags of reads that 41 tabular file with aligned families as input and prints all tags of reads that
42 carry a mutation to a user specified output file and creates a fastq file of 42 carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of
43 reads of tags with a mutation. 43 reads of tags with a mutation and the reference allele.
44 44
45 **Input** 45 **Input**
46 46
47 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. 47 **Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g.
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. 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 49
50 50
51 **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
52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. 52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
55 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline 55 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
56 <https://doi.org/10.1186/s13059-016-1039-4>`_ 56 <https://doi.org/10.1186/s13059-016-1039-4>`_
57 57
58 **Output** 58 **Output**
59 59
60 The output is a json file containing dictonaries of the tags of reads containing mutations 60 The output is a json file containing dictionaries of the tags of reads containing mutations
61 in the DCS and a fastq file of all reads of these tags. 61 in the DCS and a fastq file of all reads of these tags.
62 62
63 ]]> 63 ]]>
64 </help> 64 </help>
65 <expand macro="citation" /> 65 <expand macro="citation" />