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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
author artbio
date Sun, 13 Sep 2020 22:27:03 +0000
parents 924c527fb379
children aea952be68cb
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1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_2">
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2 <description>from genomic variations in vcf files</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
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5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
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6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
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7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
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8 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
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9 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
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10 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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11 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
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12 <!-- install bioconda genomes
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13 bioconductor-bsgenome.mmusculus.ucsc.mm9
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14 bioconductor-bsgenome.mmusculus.ucsc.mm10 -->
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15 </requirements>
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16 <stdio>
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17 <exit_code range="1:" level="fatal" description="Tool exception" />
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18 </stdio>
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19
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20 <command detect_errors="exit_code"><![CDATA[
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21 #import json
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22 #import os
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23 Rscript $__tool_directory__/mutational_patterns.R
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24 --inputs
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25 #set $filename_to_element_identifiers = {}
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26 #for $sample in $vcfs:
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27 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
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28 #end for
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29 '#echo json.dumps(filename_to_element_identifiers)#'
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30 --genome '$genome'
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31 --levels '$levels'
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32 --signum '$signum'
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33 --output '$output'
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34
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35 ]]></command>
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36 <inputs>
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37 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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38 <param name="genome" type="select" label="Reference Genome">
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39 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>
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40 <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option>
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41 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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42 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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43 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
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44 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
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45 </param>
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46 <param name="levels" type="data" format="tabular"
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47 label="A two-column tab-separated file describing levels attributed to each sample name"
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48 help="Tip: the sample name list in the vcf collection can be obtained using
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49 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
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50 example:&lt;br&gt;
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51 sample1 female&lt;br&gt;
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52 sample2 female&lt;br&gt;
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53 sample3 male&lt;br&gt;
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54 sample4 female&lt;br&gt;
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55 sample5 male&lt;br&gt;
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56 sample5 male" />
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57 <param name="signum" type="integer" value="2" min="2" max="30"
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58 label="selects the N most significant signatures in samples to express mutational patterns"
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59 help="an integer between 2 and 30 signature types from cosmic"/>
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60
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61 </inputs>
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62 <outputs>
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63 <data name="output" format="pdf" label="Mutational Patterns/Signatures" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="vcfs">
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68 <collection type="list">
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69 <element name="1" value="EGF167.vcf"/>
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70 <element name="2" value="EGF089.vcf"/>
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71 <element name="3" value="EGF037F.vcf"/>
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72 </collection>
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73 </param>
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74 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
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75 <param name="levels" value="levels.tab" ftype="tabular"/>
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76 <param name="signum" value="3" />
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77 <output name="output" file="output.pdf" compare="sim_size" ftype="pdf"/>
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78 </test>
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79 </tests>
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80 <help>
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81
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82 **What it does**
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83
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84 Takes as inputs
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85
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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86 * a collection of n vcf files corresponding to n samples.
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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87 * a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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88 * the number of cosmic signatures to decompose mutational patterns of samples
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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89
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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90
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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91 This tool returns a pdf file with the visualisation :
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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92
1
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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94 * the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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95 * the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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96 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern
0
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98
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99 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
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100
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101 </help>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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102 <citations>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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103 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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104 <citation type="doi">10.1186/s13073-018-0539-0</citation>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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105 <citation type="doi">10.1038/nature12477</citation>
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106 </citations>
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107 </tool>