Mercurial > repos > mheinzl > variant_analyzer2

annotate mut2read.xml @ 54:95c27bcb1b7a draft

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author mheinzl
date Fri, 12 Mar 2021 08:00:31 +0000
parents d21960b45a6b
children 3691922baa08
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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="2.0.1" 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 <requirements>
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8 <requirement type="package" version="2.7">python</requirement>
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9 <requirement type="package" version="1.4.0">matplotlib</requirement>
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10 <requirement type="package" version="0.15">pysam</requirement>
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11 <requirement type="package" version="0.11.6">cyvcf2</requirement>
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12 </requirements>
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13 <command><![CDATA[
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14 ln -s '$file2' bam_input.bam &&
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15 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
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16 python '$__tool_directory__/mut2read.py'
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17 --mutFile '$file1'
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18 --bamFile bam_input.bam
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19 --familiesFile '$file3'
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20 --outputFastq '$output_fastq'
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21 --outputJson '$output_json'
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See Help section below for a detailed explanation."/>
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26 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
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27 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
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28 </inputs>
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29 <outputs>
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30 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
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31 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="file1" value="FreeBayes_test.vcf" lines_diff="2"/>
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36 <param name="file2" value="DCS_test.bam"/>
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37 <param name="file3" value="Aligned_Families_test.tabular"/>
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38 <output name="output_fastq" file="Interesting_Reads_test.fastq" lines_diff="136"/>
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39 <output name="output_json" file="tag_count_dict_test.json" lines_diff="2"/>
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40 </test>
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41 </tests>
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42 <help> <![CDATA[
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43 **What it does**
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44
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45 Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a
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46 tabular file with aligned families as input and prints all tags of reads that
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47 carry a mutation to a user specified output file and creates a fastq file of
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48 reads of tags with a mutation.
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49
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50 **Input**
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51
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52 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
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53 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
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54
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55 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the
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56 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
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57
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58 **Dataset 3:** Tabular file with reads as produced by the
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59 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline
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60 <https://doi.org/10.1186/s13059-016-1039-4>`_
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61
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62 **Output**
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63
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64 The output is a json file containing dictonaries of the tags of reads containing mutations
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65 in the DCS and a fastq file of all reads of these tags.
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66
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67 ]]>
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68 </help>
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69 <expand macro="citation" />
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70 </tool>