annotate read2mut.xml @ 77:1797e461d674 draft default tip

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 29 Mar 2021 09:22:57 +0000
parents 56f271641828
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="read2mut" name="Call specific mutations in reads:" version="2.1.4" profile="19.01">
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3 <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</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 <requirement type="package" version="1.1.0">xlsxwriter</requirement>
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9 </expand>
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10 <command><![CDATA[
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11 ln -s '$file2' bam_input.bam &&
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12 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
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13 python '$__tool_directory__/read2mut.py'
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14 --mutFile '$file1'
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15 --bamFile bam_input.bam
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16 --inputJson '$file3'
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17 --sscsJson '$file4'
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18 --thresh '$thresh'
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19 --phred '$phred'
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20 --trim '$trim'
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21 $chimera_correction
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22 --softclipping_dist '$softclipping_dist'
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23 --reads_threshold '$reads_threshold'
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24 --outputFile '$output_xlsx'
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25 --outputFile_csv '$outputFile_csv'
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26 --outputFile2 '$output_xlsx2'
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27 --outputFile3 '$output_xlsx3'
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28 ]]>
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29 </command>
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30 <inputs>
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31 <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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32 <param name="file2" type="data" format="bam" label="BAM File of raw reads" optional="false" help="BAM file with aligned raw reads of selected tags."/>
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33 <param name="file3" type="data" format="json" label="JSON File with DCS tag stats" optional="false" help="JSON file generated by DCS mutations to tags/reads"/>
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34 <param name="file4" type="data" format="json" label="JSON File with SSCS tag stats" optional="false" help="JSON file generated by DCS mutations to SSCS stats."/>
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35 <param name="thresh" type="integer" label="Tag count threshold" value="0" help="Integer threshold for displaying mutations. Only mutations occuring in DCS of less than thresh tags are displayed. Default of 0 displays all."/>
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36 <param name="phred" type="integer" label="Phred quality score threshold" min="0" max="41" value="20" help="Integer threshold for Phred quality score. Only reads higher than this threshold are considered. Default = 20."/>
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37 <param name="trim" type="integer" label="Trimming threshold" value="10" help="Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10."/>
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38 <param name="chimera_correction" type="boolean" label="Apply chimera correction?" truevalue="--chimera_correction" falsevalue="" checked="False" help="Count chimeric variants and correct the variant frequencies."/>
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39 <param name="softclipping_dist" type="integer" label="Distance between artifact and softclipping of the reads" min="1" value="15" help="Count mutation as an artifact if mutation lies within this parameter away from the softclipping part of the reads. Default = 20"/>
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40 <param name="reads_threshold" type="float" label="Minimum percentage of softclipped reads in a family" min="0.0" max="1.0" value="1.0" help="Float number which specifies the minimum percentage of softclipped reads in a family to be considered in the softclipping tiers. Default: 1.0, means all reads of a family have to be softclipped."/>
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41 </inputs>
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42 <outputs>
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43 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
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44 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
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45 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
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46 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="file1" value="FreeBayes_test.vcf"/>
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51 <param name="file2" value="Interesting_Reads_test.trim.bam"/>
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52 <param name="file3" value="tag_count_dict_test.json"/>
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53 <param name="file4" value="SSCS_counts_test.json"/>
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54 <param name="thresh" value="0"/>
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55 <param name="phred" value="20"/>
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56 <param name="trim" value="10"/>
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57 <param name="chimera_correction"/>
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58 <param name="softclipping_dist" value="15"/>
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59 <param name="reads_threshold" value="1.0"/>
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60 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
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61 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
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62 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
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63 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
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64 </test>
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65 </tests>
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66 <help> <![CDATA[
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67 **What it does**
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68
6
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69 Takes a VCF file with mutations, a BAM file of aligned raw reads, and JSON files
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70 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats**
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71 as input and calculates frequencies and stats for DCS mutations based on information
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72 from the raw reads.
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73
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74 **Input**
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75
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76 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
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77 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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78
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79 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
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80 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
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81
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82 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
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83 containing dictonaries of the tags of reads containing mutations
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84 in the DCS.
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85
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86 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
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87 stats of tags that carry a mutation in the SSCS at the same position a mutation
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88 is called in the DCS.
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89
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90 **Output**
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91
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92 The output are three XLSX files containing frequencies stats for DCS mutations based
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93 on information from the raw reads and a CSV file containing the summary information without color-coding. In addition to that a tier based
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94 classification is provided based on the amout of support for a true variant call.
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95
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96
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97 ]]>
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98 </help>
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99 <expand macro="citation" />
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100 </tool>