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annotate mutational_patterns.xml @ 11:7995a949189f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
author artbio
date Thu, 22 Oct 2020 00:18:38 +0000
parents 59c0e2a7965c
children 7954f0d3517f
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy12">
0
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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>
2
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8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
0
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9 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
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10 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
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11 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
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13 <!-- install bioconda genomes
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14 bioconductor-bsgenome.mmusculus.ucsc.mm9
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15 bioconductor-bsgenome.mmusculus.ucsc.mm10 -->
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16 </requirements>
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17 <stdio>
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18 <exit_code range="1:" level="fatal" description="Tool exception" />
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19 </stdio>
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21 <command detect_errors="exit_code"><![CDATA[
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22 #import json
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23 #import os
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24 Rscript $__tool_directory__/mutational_patterns.R
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25 --inputs
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26 #set $filename_to_element_identifiers = {}
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27 #for $sample in $vcfs:
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28 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
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29 #end for
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30 '#echo json.dumps(filename_to_element_identifiers)#'
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31 --genome '$genome'
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32
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33 #if $set_levels.choices == 'yes':
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34 --levels '$set_levels.levels'
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35 #end if
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36
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37 #if $set_spectrum.choices == 'yes':
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38 --output_spectrum $spectrum
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39 #end if
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40
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41 #if $set_denovo.choices == 'yes':
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42 --nrun $set_denovo.nrun
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43 --rank $set_denovo.rank
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44 --newsignum $set_denovo.newsignum
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45 --output_denovo $denovo
3
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46 --sigmatrix $sigmatrix
2
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47 #end if
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48
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49 #if $set_cosmic.choices == 'yes':
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50 --cosmic_version '$set_cosmic.cosmic_version'
2
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51 --signum '$set_cosmic.signum'
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52 --output_cosmic $cosmic
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53 #if $set_cosmic.contrib_matrix_out
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54 --sig_contrib_matrix $sig_contrib_matrix
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55 #end if
2
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56 #end if
0
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57
3
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58 #if $rdata_out
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59 --rdata '$rdata'
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60 #end if
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61
0
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62 ]]></command>
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63 <inputs>
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64 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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65 <param name="genome" type="select" label="Reference Genome">
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66 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>
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67 <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option>
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68 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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69 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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70 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
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71 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
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72 </param>
2
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73 <conditional name="set_levels">
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74 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
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75 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
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76 <option value="no" selected="true">No</option>
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77 <option value="yes">Yes</option>
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78 </param>
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79 <when value="yes">
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80 <param name="levels" type="data" format="tabular"
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81 label="A two-column tab-separated file describing levels attributed to each sample name"
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82 help="Tip: the sample name list in the vcf collection can be obtained using
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83 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
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parents: 1
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84 example:&lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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85 sample1 female&lt;br&gt;
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artbio
parents: 1
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86 sample2 female&lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
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87 sample3 male&lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
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88 sample4 female&lt;br&gt;
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artbio
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89 sample5 male&lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
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90 sample5 male" />
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91 </when>
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artbio
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92 <when value="no" />
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93 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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94 <conditional name="set_spectrum">
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artbio
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95 <param name="choices" type="select" label="Analyse Mutational Spectrum" display="radio">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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96 <option value="yes" selected="true">Yes</option>
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artbio
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97 <option value="no">No</option>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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98 </param>
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artbio
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99 <when value="yes" />
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100 <when value="no" />
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101 </conditional>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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102
2
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artbio
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103 <conditional name="set_denovo">
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104 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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105 <option value="yes" selected="true">Yes</option>
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106 <option value="no">No</option>
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107 </param>
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108 <when value="yes">
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109 <param name="nrun" type="integer" value="10" min="10" max="200"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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110 label="Number of cycles to find best fitting of signatures"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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diff changeset
111 help="High values extend the computational time"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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112 <param name="rank" type="integer" value="4" min="3" max="30"
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artbio
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113 label="Number of ranks to be displayed for control of optimal number of signature"
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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114 help="High values extend the computational time. In addition the number of ranks cannot be greater than the number of available samples in the study"/>
2
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115 <param name="newsignum" type="integer" value="4" min="2" max="30"
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116 label="Number of de novo signatures to capture"
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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117 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
2
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118 </when>
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119 <when value="no" />
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120 </conditional>
0
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121
2
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122 <conditional name="set_cosmic">
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123 <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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124 <option value="yes" selected="true">Yes</option>
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125 <option value="no">No</option>
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126 </param>
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127 <when value="yes">
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128 <param name="signum" type="integer" value="3" min="2" max="30"
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129 label="selects the N most significant signatures in samples to express mutational patterns"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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130 help="an integer between 2 and 30 signature types from cosmic"/>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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131 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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132 <option value="v2" selected="true">Cosmic v2, March 2015</option>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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133 <option value="v3">Cosmic v3, May 2019</option>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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134 </param>
11
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135 <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?"
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136 help="Output the normalized signatures contributions for further visualization" />
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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137 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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138 <when value="no" />
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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139 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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140 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
0
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141 </inputs>
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142 <outputs>
2
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143 <data name="spectrum" format="pdf" label="Mutational Spectrum">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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144 <filter>set_spectrum['choices'] == "yes"</filter>
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145 </data>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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146 <data name="denovo" format="pdf" label="De novo signatures">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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147 <filter>set_denovo['choices'] == "yes"</filter>
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artbio
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148 </data>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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149 <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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150 <filter>set_denovo['choices'] == "yes"</filter>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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diff changeset
151 </data>
2
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parents: 1
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152 <data name="cosmic" format="pdf" label="Cosmic signatures">
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153 <filter>set_cosmic['choices'] == "yes"</filter>
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artbio
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diff changeset
154 </data>
11
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155 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
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156 <filter>set_cosmic['contrib_matrix_out']</filter>
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artbio
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diff changeset
157 </data>
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158
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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diff changeset
159 <data name="rdata" format="rdata" label="${tool.name}: RData file">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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160 <filter>rdata_out</filter>
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artbio
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161 </data>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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162
0
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163 </outputs>
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164 <tests>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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165 <!-- simple profile -->
2
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166 <test>
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167 <param name="vcfs">
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168 <collection type="list">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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169 <element name="1" ftype="vcf" value="G.vcf"/>
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diff changeset
170 <element name="2" ftype="vcf" value="H.vcf"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
171 </collection>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
172 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
173 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
174 <conditional name="set_levels">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
175 <param name="choices" value="yes"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
176 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
177 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
178 <conditional name="set_spectrum">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
179 <param name="choices" value="yes"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
180 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
181 <conditional name="set_denovo">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
182 <param name="choices" value="no"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
183 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
184 <conditional name="set_cosmic">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
185 <param name="choices" value="no"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
186 </conditional>
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
187 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
188 </test>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
189
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
190 <!-- de novo signatures -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
191 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
192 <param name="vcfs">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
193 <collection type="list">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
194 <element name="6" value="F.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
195 <element name="7" value="G.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
196 <element name="8" value="H.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
197 <element name="9" value="I.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
198 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
199 </param>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
200 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
201 <conditional name="set_spectrum">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
202 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
203 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
204 <conditional name="set_denovo">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
205 <param name="choices" value="yes"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
206 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
207 <conditional name="set_cosmic">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
208 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
209 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
210 <param name="nrun" value="10" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
211 <param name="rank" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
212 <param name="newsignum" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
213 <param name="rdata_out" value="true" />
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
214 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
215 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
216 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
217 </test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
218
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
219 <!-- cosmic signatures -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
220 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
221 <param name="vcfs">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
222 <collection type="list">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
223 <element name="6" value="F.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
224 <element name="7" value="G.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
225 <element name="8" value="H.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
226 <element name="9" value="I.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
227 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
228 </param>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
229 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
4
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
230 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
231 <conditional name="set_spectrum">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
232 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
233 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
234 <conditional name="set_denovo">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
235 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
236 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
237 <conditional name="set_cosmic">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
238 <param name="choices" value="yes"/>
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
239 <param name="contrib_matrix_out" value="true" />
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
240 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
241 <param name="signum" value="3" />
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
242 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
243 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
244 </test>
8
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
parents: 7
diff changeset
245 <!-- cosmic signature on single sample -->
4
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
246 <test>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
247 <param name="vcfs">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
248 <collection type="list">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
249 <element name="1" value="G.vcf"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
250 </collection>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
251 </param>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
252 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
253 <conditional name="set_spectrum">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
254 <param name="choices" value="no"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
255 </conditional>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
256 <conditional name="set_denovo">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
257 <param name="choices" value="no"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
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258 </conditional>
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259 <conditional name="set_cosmic">
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260 <param name="choices" value="yes"/>
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261 </conditional>
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262 <param name="signum" value="5" />
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263 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
4
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264 </test>
0
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265 </tests>
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266 <help>
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267
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268 **What it does**
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269
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270 Takes as inputs
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271
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272 * a collection of n vcf files corresponding to n samples.
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273 * a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
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274 * the number of cosmic signatures to decompose mutational patterns of samples
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275
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276
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277 This tool returns a pdf file with the visualisation :
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278
1
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279 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
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280 * 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)
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281 * 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)
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282 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
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283 * 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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284
1
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285 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
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286
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287 </help>
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288 <citations>
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289 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
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290 <citation type="doi">10.1186/s13073-018-0539-0</citation>
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291 <citation type="doi">10.1038/nature12477</citation>
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292 </citations>
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293 </tool>