Mercurial > repos > mheinzl > variant_analyzer2

annotate read2mut.xml @ 5:d9cbf833624e draft

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planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Tue, 27 Oct 2020 12:46:55 +0000
parents 386438cd4c3b
children 11a2a34f8a2b
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1 <?xml version="1.0" encoding="UTF-8"?>
4
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2 <tool id="read2mut" name="Call specific mutations in reads:" version="1.0.5" profile="19.01">
0
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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 '$file2' bam_input.bam &&
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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12 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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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
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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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 $chimera_correction
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22 --outputFile '$output_xlsx'
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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27 <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."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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28 <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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29 <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."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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30 <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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31 <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."/>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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32 <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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33 <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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34 </inputs>
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35 <outputs>
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36 <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/>
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41 <param name="file2" value="Interesting_Reads_test_data_VA.trim.bam"/>
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42 <param name="file3" value="tag_count_dict_test_data_VA.json"/>
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43 <param name="file4" value="SSCS_counts_test_data_VA.json"/>
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44 <param name="thresh" value="0"/>
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45 <param name="phred" value="20"/>
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46 <param name="trim" value="10"/>
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47 <param name="chimera_correction" value="False"/>
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48 <output name="output_xlsx" file="mutant_reads_summary_short_trim_test_data_VA.xlsx" decompress="true" lines_diff="10"/>
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49 </test>
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50 </tests>
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51 <help> <![CDATA[
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52 **What it does**
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53
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54 Takes a tabular file with mutations, a BAM file of aligned raw reads, and JSON files
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55 created by the tools **DCS mutations to tags/reads** and **DCS mutations to SSCS stats**
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56 as input and calculates frequencies and stats for DCS mutations based on information
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57 from the raw reads.
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58
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59 **Input**
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60
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61 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as
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62 generated by the **Variant Annotator** tool.
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63
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64 **Dataset 2:** BAM file of aligned raw reads. This file can be obtained by the
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65 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_.
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66
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67 **Dataset 3:** JSON file generated by the **DCS mutations to tags/reads** tool
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68 containing dictonaries of the tags of reads containing mutations
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69 in the DCS.
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70
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71 **Dataset 4:** JSON file generated by the **DCS mutations to SSCS stats** tool
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72 stats of tags that carry a mutation in the SSCS at the same position a mutation
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73 is called in the DCS.
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74
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75 **Output**
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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76
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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77 The output is an XLSX file containing frequencies stats for DCS mutations based
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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78 on information from the raw reads. In addition to that a tier based
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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79 classification is provided based on the amout of support for a true variant call.
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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80
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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81 ]]>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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82 </help>
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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83 <expand macro="citation" />
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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84 </tool>