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comparison mut2read.xml @ 84:e46d5e377760 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, 19 Aug 2022 11:23:37 +0000
parents fdfe9a919ff7
children 97bd9c7a1b44
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83:8cec772c0bf1 84:e46d5e377760
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="3.0.0" profile="19.01"> 2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="3.1.0" 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 <expand macro="requirements"/> 7 <expand macro="requirements"/>
10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && 10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
11 python '$__tool_directory__/mut2read.py' 11 python '$__tool_directory__/mut2read.py'
12 --mutFile '$file1' 12 --mutFile '$file1'
13 --bamFile bam_input.bam 13 --bamFile bam_input.bam
14 --familiesFile '$file3' 14 --familiesFile '$file3'
15 $refalttiers
15 --outputFastq '$output_fastq' 16 --outputFastq '$output_fastq'
16 --outputJson '$output_json' 17 --outputJson '$output_json'
17 ]]> 18 ]]>
18 </command> 19 </command>
19 <inputs> 20 <inputs>
20 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/> 21 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> 22 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> 23 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
24 <param name="refalttiers" type="boolean" label="Extract tiers also for reference allele" truevalue="--refalttiers" falsevalue="" checked="False" help="Extracts tier information for the alternate and reference allele. Note that this will increase the running time of the tool. Otherwise only the tier information for the alternate allele is extracted."/>
23 </inputs> 25 </inputs>
24 <outputs> 26 <outputs>
25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> 27 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> 28 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
27 </outputs> 29 </outputs>
38 **What it does** 40 **What it does**
39 41
40 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 42 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 43 tabular file with aligned families as input and prints all tags of reads that
42 carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of 44 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 and the reference allele. 45 reads of tags with a mutation (and optional the reference allele).
44 46
45 **Input** 47 **Input**
46 48
47 **Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g. 49 **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. 50 generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.