Mercurial > repos > mheinzl > variant_analyzer2

annotate read2mut.xml @ 32:80cbf0bd6e9c draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Wed, 24 Feb 2021 10:59:04 +0000
parents afda74e874ac
children da224c392a54
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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="2.0.4" profile="17.01">
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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 --trim5 '$trim5'
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21 --trim3 '$trim3'
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22 $chimera_correction
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23 --outputFile '$output_xlsx'
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24 --outputFile_csv '$outputFile_csv'
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25 --outputFile2 '$output_xlsx2'
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26 --outputFile3 '$output_xlsx3'
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27 ]]>
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28 </command>
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29 <inputs>
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30 <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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31 <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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32 <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"/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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33 <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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34 <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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35 <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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36 <param name="trim5" type="integer" label="Trimming threshold at 5' end" value="10" help="Integer threshold for assigning mutations at the beginning of reads to lower tier. Default 10."/>
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37 <param name="trim3" type="integer" label="Trimming threshold at 3' end" value="10" help="Integer threshold for assigning mutations at the 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 </inputs>
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40 <outputs>
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41 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
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42 <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
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43 <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
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44 <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="file1" value="FreeBayes_test.vcf"/>
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49 <param name="file2" value="Interesting_Reads_test.trim.bam"/>
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50 <param name="file3" value="tag_count_dict_test.json"/>
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51 <param name="file4" value="SSCS_counts_test.json"/>
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52 <param name="thresh" value="0"/>
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53 <param name="phred" value="20"/>
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54 <param name="trim5" value="10"/>
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55 <param name="trim3" value="10"/>
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56 <param name="delim_csv" value=","/>
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57 <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
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58 <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
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59 <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
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60 <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
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61 </test>
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62 </tests>
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63 <help> <![CDATA[
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64 **What it does**
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65
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66 Takes a VCF file with mutations, a BAM file of aligned raw reads, and JSON files
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67 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats**
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68 as input and calculates frequencies and stats for DCS mutations based on information
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69 from the raw reads.
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70
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71 **Input**
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72
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73 **Dataset 1:** VCF file with duplex consesus sequence (DCS) mutations. E.g.
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74 generated by the `FreeBayes variant caller <https://arxiv.org/abs/1207.3907>`_.
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75
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76 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
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77 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
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78
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79 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
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80 containing dictonaries of the tags of reads containing mutations
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81 in the DCS.
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82
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83 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
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84 stats of tags that carry a mutation in the SSCS at the same position a mutation
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85 is called in the DCS.
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86
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87 **Output**
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88
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89 The output are three XLSX files containing frequencies stats for DCS mutations based
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90 on information from the raw reads. In addition to that a tier based
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91 classification is provided based on the amout of support for a true variant call.
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92
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93 ]]>
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94 </help>
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95 <expand macro="citation" />
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96 </tool>