Mercurial > repos > mheinzl > variant_analyzer2
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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
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date | Mon, 22 Feb 2021 16:31:04 +0000 |
parents | 84a1a3f70407 |
children | d21960b45a6b |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="mut2read" name="DCS mutations to tags/reads:" version="2.0.1" profile="19.01"> <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> <macros> <import>va_macros.xml</import> </macros> <expand macro="requirements"/> <command><![CDATA[ ln -s '$file2' bam_input.bam && ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && python '$__tool_directory__/mut2read.py' --mutFile '$file1' --bamFile bam_input.bam --familiesFile '$file3' --outputFastq '$output_fastq' --outputJson '$output_json' ]]> </command> <inputs> <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/> <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> </inputs> <outputs> <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> </outputs> <tests> <test> <param name="file1" value="FreeBayes_test.vcf"/> <param name="file2" value="DCS_test.bam"/> <param name="file3" value="Aligned_Families_test.tabular"/> <output name="output_fastq" file="Interesting_Reads_test.fastq"/> <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/> </test> </tests> <help> <![CDATA[ **What it does** Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a tabular file with aligned families as input and prints all tags of reads that carry a mutation to a user specified output file and creates a fastq file of reads of tags with a mutation. **Input** **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g. generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_. **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. **Dataset 3:** Tabular file with reads as produced by the **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline <https://doi.org/10.1186/s13059-016-1039-4>`_ **Output** The output is a json file containing dictonaries of the tags of reads containing mutations in the DCS and a fastq file of all reads of these tags. ]]> </help> <expand macro="citation" /> </tool>