Mercurial > repos > mheinzl > variant_analyzer2

annotate mut2read.xml @ 78:fdfe9a919ff7 draft

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author mheinzl
date Fri, 22 Jul 2022 09:19:44 +0000
parents 6ccff403db8a
children e46d5e377760
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="3.0.0" profile="19.01">
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3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
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4 <macros>
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5 <import>va_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 ln -s '$file2' bam_input.bam &&
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10 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
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11 python '$__tool_directory__/mut2read.py'
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12 --mutFile '$file1'
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13 --bamFile bam_input.bam
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14 --familiesFile '$file3'
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15 --outputFastq '$output_fastq'
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16 --outputJson '$output_json'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
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21 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
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22 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
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23 </inputs>
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24 <outputs>
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25 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
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26 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="file1" value="FreeBayes_test.vcf"/>
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31 <param name="file2" value="DCS_test.bam"/>
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32 <param name="file3" value="Aligned_Families_test.tabular"/>
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33 <output name="output_fastq" file="Interesting_Reads_test.fastq"/>
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34 <output name="output_json" file="tag_count_dict_test.json"/>
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35 </test>
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36 </tests>
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37 <help> <![CDATA[
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38 **What it does**
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39
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40 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a
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41 tabular file with aligned families as input and prints all tags of reads that
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42 carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of
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43 reads of tags with a mutation and the reference allele.
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45 **Input**
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47 **Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g.
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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.
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49
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51 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the
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52 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
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54 **Dataset 3:** Tabular file with reads as produced by the
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55 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
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56 <https://doi.org/10.1186/s13059-016-1039-4>`_
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58 **Output**
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59
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60 The output is a json file containing dictionaries of the tags of reads containing mutations
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61 in the DCS and a fastq file of all reads of these tags.
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63 ]]>
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64 </help>
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65 <expand macro="citation" />
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66 </tool>