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annotate mutational_patterns.xml @ 19:69f09dff98f9 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26"
author artbio
date Sun, 17 Oct 2021 23:05:01 +0000
parents 8d9f31389f33
children a2cb7dc9250a
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69f09dff98f9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26"
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy4">
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="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
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5 <requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement>
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6 <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement>
15
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7 <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
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8 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
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9 <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
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10 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
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11 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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12 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
14
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13 <!--
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14 install more bioconda genomes
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15 bioconductor-bsgenome.mmusculus.ucsc.mm9
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16 bioconductor-bsgenome.mmusculus.ucsc.mm10
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17 -->
0
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18 </requirements>
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19 <stdio>
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20 <exit_code range="1:" level="fatal" description="Tool exception" />
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21 </stdio>
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14
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23 <command detect_errors="exit_code"><![CDATA[
0
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24 #import json
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25 #import os
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26 Rscript $__tool_directory__/mutational_patterns.R
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27 --inputs
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28 #set $filename_to_element_identifiers = {}
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29 #for $sample in $vcfs:
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30 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
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31 #end for
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32 '#echo json.dumps(filename_to_element_identifiers)#'
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33 --genome '$genome'
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35 #if $set_levels.choices == 'yes':
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36 --levels '$set_levels.levels'
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37 #end if
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38
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39 #if $set_spectrum.choices == 'yes':
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40 --output_spectrum $spectrum
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41 #end if
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43 #if $set_denovo.choices == 'yes':
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44 --nrun $set_denovo.nrun
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45 --rank $set_denovo.rank
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46 --newsignum $set_denovo.newsignum
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47 --output_denovo $denovo
3
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48 --sigmatrix $sigmatrix
2
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49 #end if
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50
18
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51 #if $set_preset.choices == 'yes':
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52
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53 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'
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54 --cosmic_version '$set_preset.set_signature_input.cosmic_version'
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55 #end if
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56
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57 #if $set_preset.set_signature_input.input_signature_choices == 'user_signatures'
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58 --own_signatures '$set_preset.set_signature_input.own_matrix'
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59 #end if
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60
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61 --signum '$set_preset.signum'
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62 --output_sigpattern $sig_contrib
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63
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
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64 #if $set_preset.contrib_matrix_out == 'yes'
11
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65 --sig_contrib_matrix $sig_contrib_matrix
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66 #end if
18
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67
2
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68 #end if
0
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69
3
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70 #if $rdata_out
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71 --rdata '$rdata'
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72 #end if
17
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73
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74 --tooldir '$__tool_directory__/'
3
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75
0
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76 ]]></command>
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77 <inputs>
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78 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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79 <param name="genome" type="select" label="Reference Genome">
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80 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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81 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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82 </param>
2
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83 <conditional name="set_levels">
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84 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
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parents: 1
diff changeset
85 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
86 <option value="no" selected="true">No</option>
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artbio
parents: 1
diff changeset
87 <option value="yes">Yes</option>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
88 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
89 <when 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
90 <param name="levels" type="data" format="tabular"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
91 label="A two-column tab-separated file describing levels attributed to each sample name"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
92 help="Tip: the sample name list in the vcf collection can be obtained using
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
93 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
94 example:&lt;br&gt;
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
95 sample1 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
diff changeset
96 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
diff changeset
97 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
diff changeset
98 sample4 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
diff changeset
99 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
diff changeset
100 sample5 male" />
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
101 </when>
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artbio
parents: 1
diff changeset
102 <when 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
103 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
104 <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
105 <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
parents: 1
diff changeset
106 <option value="yes" selected="true">Yes</option>
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artbio
parents: 1
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107 <option value="no">No</option>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
108 </param>
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artbio
parents: 1
diff changeset
109 <when value="yes" />
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artbio
parents: 1
diff changeset
110 <when value="no" />
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artbio
parents: 1
diff changeset
111 </conditional>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
112
2
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artbio
parents: 1
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113 <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
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114 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
115 <option value="yes">Yes</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
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116 <option value="no" selected="true">No</option>
2
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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117 </param>
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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118 <when value="yes">
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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119 <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
parents: 1
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120 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
parents: 1
diff changeset
121 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"
artbio
parents: 1
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122 <param name="rank" type="integer" value="4" min="3" max="30"
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artbio
parents: 1
diff changeset
123 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"
artbio
parents: 2
diff changeset
124 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
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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125 <param name="newsignum" type="integer" value="4" min="2" max="30"
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
126 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"
artbio
parents: 2
diff changeset
127 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
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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128 </when>
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artbio
parents: 1
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129 <when value="no" />
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artbio
parents: 1
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130 </conditional>
0
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131
18
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artbio
parents: 17
diff changeset
132 <conditional name="set_preset">
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artbio
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133 <param name="choices" type="select" label="Decompose with preset signatures" display="radio">
2
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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134 <option value="yes" selected="true">Yes</option>
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artbio
parents: 1
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135 <option value="no">No</option>
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artbio
parents: 1
diff changeset
136 </param>
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artbio
parents: 1
diff changeset
137 <when value="yes">
18
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artbio
parents: 17
diff changeset
138 <conditional name="set_signature_input">
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artbio
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139 <param name="input_signature_choices" type="select" label="type of signatures" display="radio">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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140 <option value="cosmic" selected="true">COSMIC signatures</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
141 <option value="user_signatures">Use your own signature matrix</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
142 </param>
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artbio
parents: 17
diff changeset
143 <when value="cosmic">
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artbio
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diff changeset
144 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
145 <option value="v2" selected="true">Cosmic v2, March 2015</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
146 <option value="v3">Cosmic v3, May 2019</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
147 <option value="v3.1">Cosmic v3.1, June 2020</option>
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artbio
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diff changeset
148 <option value="v3.2">Cosmic v3.2, March 2021</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
149 </param>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
150 </when>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
151 <when value="user_signatures">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
152 <param name="own_matrix" type="data" format="tabular"
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
153 label="A tab-separated matrix describing elementary signatures"
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
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diff changeset
154 help="see https://cancer.sanger.ac.uk/signatures/documents/453/COSMIC_v3.2_SBS_GRCh38.txt for the required format" />
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artbio
parents: 17
diff changeset
155 </when>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
156 </conditional>
2
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artbio
parents: 1
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157 <param name="signum" type="integer" value="3" min="2" max="30"
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artbio
parents: 1
diff changeset
158 label="selects the N most significant signatures in samples to express mutational patterns"
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
159 help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
15
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artbio
parents: 14
diff changeset
160 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
161 help="Output the normalized signatures contributions for further visualization" >
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artbio
parents: 14
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162 <option value="no" selected="true">No</option>
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artbio
parents: 14
diff changeset
163 <option value="yes">Yes</option>
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artbio
parents: 14
diff changeset
164 </param>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
165 </when>
18
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artbio
parents: 17
diff changeset
166 <when value="no" />
3
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artbio
parents: 2
diff changeset
167 </conditional>
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parents: 2
diff changeset
168 <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
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
169 </inputs>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
170 <outputs>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
171 <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"
artbio
parents: 1
diff changeset
172 <filter>set_spectrum['choices'] == "yes"</filter>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
173 </data>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
174 <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"
artbio
parents: 1
diff changeset
175 <filter>set_denovo['choices'] == "yes"</filter>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
176 </data>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
177 <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
parents: 2
diff changeset
178 <filter>set_denovo['choices'] == "yes"</filter>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
179 </data>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
180 <data name="sig_contrib" format="pdf" label="Signature contributions">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
181 <filter>set_preset['choices'] == "yes"</filter>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
182 </data>
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
183 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
184 <filter>set_preset['choices'] == "yes" and set_preset['contrib_matrix_out'] == "yes"</filter>
11
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
185 </data>
7995a949189f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
artbio
parents: 10
diff changeset
186
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
187 <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"
artbio
parents: 2
diff changeset
188 <filter>rdata_out</filter>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
189 </data>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
190
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
191 </outputs>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
192 <tests>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
193 <!-- user defined (v3.2 restricted 30 minus 27) -->
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
194 <test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
195 <param name="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
196 <collection type="list">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
197 <element name="6" value="F.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
198 <element name="7" value="G.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
199 <element name="8" value="H.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
200 <element name="9" value="I.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
201 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
202 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
203 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
204 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
205 <conditional name="set_spectrum">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
206 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
207 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
208 <conditional name="set_denovo">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
209 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
210 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
211 <conditional name="set_preset">
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
212 <param name="choices" value="yes"/>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
213 <conditional name="set_signature_input">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
214 <param name="input_signature_choices" value="user_signatures" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
215 <param name="own_matrix" value="user_defined_signature.tsv" ftype="tabular"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
216 </conditional>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
217 <param name="contrib_matrix_out" value="yes" />
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
218 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
219 <param name="signum" value="4" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
220 <output name="sig_contrib" file="user_output.pdf" compare="sim_size"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
221 <output name="sig_contrib_matrix" file="sig_contrib_table_user_defined.tsv" compare="sim_size"/>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
222 </test>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
223 <!-- cosmic v3.2 -->
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
224 <test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
225 <param name="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
226 <collection type="list">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
227 <element name="6" value="F.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
228 <element name="7" value="G.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
229 <element name="8" value="H.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
230 <element name="9" value="I.vcf"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
231 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
232 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
233 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
234 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
235 <conditional name="set_spectrum">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
236 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
237 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
238 <conditional name="set_denovo">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
239 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
240 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
241 <conditional name="set_preset">
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
242 <param name="choices" value="yes"/>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
243 <conditional name="set_signature_input">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
244 <param name="input_signature_choices" value="cosmic" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
245 <param name="cosmic_version" value="v3.2"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
246 </conditional>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
247 <param name="contrib_matrix_out" value="yes" />
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
248 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
249 <param name="signum" value="3" />
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
250 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
251 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
252 </test>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
253 <!-- cosmic v2 -->
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
254 <test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
255 <param name="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
256 <collection type="list">
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
257 <element name="6" value="F.vcf"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
258 <element name="7" value="G.vcf"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
259 <element name="8" value="H.vcf"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
260 <element name="9" value="I.vcf"/>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
261 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
262 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
263 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
264 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
265 <conditional name="set_spectrum">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
266 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
267 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
268 <conditional name="set_denovo">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
269 <param name="choices" value="no"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
270 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
271 <conditional name="set_preset">
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
272 <param name="choices" value="yes"/>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
273 <conditional name="set_signature_input">
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
274 <param name="input_signature_choices" value="cosmic" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
275 <param name="cosmic_version" value="v2"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
276 </conditional>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
277 <param name="contrib_matrix_out" value="yes" />
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
278 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
279 <param name="signum" value="3" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
280 <output name="sig_contrib" file="cosmic_output1.pdf" compare="sim_size"/>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
281 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
282 </test>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
283 <!-- simple spectrum -->
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
284 <test>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
285 <param name="vcfs">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
286 <collection type="list">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
287 <element name="1" ftype="vcf" value="G.vcf"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
288 <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
289 </collection>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
290 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
291 <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
292 <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
293 <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
294 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
295 <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
296 <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
297 <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
298 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
299 <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
300 <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
301 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
302 <conditional name="set_preset">
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
303 <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
304 </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
305 <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
306 </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
307 <!-- 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
308 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
309 <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
310 <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
311 <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
312 <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
313 <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
314 <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
315 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
316 </param>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
317 <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
318 <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
319 <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
320 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
321 <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
322 <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
323 </conditional>
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
324 <conditional name="set_preset">
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
325 <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
326 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
327 <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
328 <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
329 <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
330 <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
331 <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
332 <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
333 <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
334 </test>
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
335 </tests>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
336 <help>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
337
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
338 **What it does**
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
339
18
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
340 This tool implement the R package MutationalPatterns to decompose mutations found in cancers
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
341 in a linear combination of elementary mutational signatures, as first described by
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342 Alexandrov_ et al (2013) and recently improved in an update_ published in 2020.
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343
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344 .. _Alexandrov: https://www.nature.com/articles/nature12477
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345 .. _update: https://www.nature.com/articles/s41586-020-1943-3
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346
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347 Sets of elementary signatures found by analyzing large cohortes of patients are published
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348 in the COSMIC databases v2_ to v3.2_. You can choose among these COSMIC signature sets to
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349 analyse your own VCFs.
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350
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351 In addition, you can use your own signature sets (or filtered COSMIC signature sets)
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352 since MutationalPatterns implements a method to extract elementary signatures from
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353 user-provided VCFs.
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354
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355 **Inputs**
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356
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357 * a collection of VCF files with somatic mutations calls from analysis of samples.
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358 * a tabular table describing the correspondance of sample names to levels of a factor
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359 (tissues, ages, sexes, etc.)
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360
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361 **Outputs**
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362
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363 This tool returns pdf files with various visualisations of :
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364
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365 * the spectrum of single nucleotide mutation types
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366 * the absolute contribution of the elementary signatures in the samples
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367 * the relative contribution of the elementary signatures in the samples
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368 * an unrooted hierarchical clustering of the reconstructed samples with respect to the relative contribution of elementary signatures
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369 * the Cosine similarity between true samples and samples reconstructed with elementary signatures
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370 * pie charts displaying the relative contribution of the n most contributing elementary signatures in the reconstructed sample profiles
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371
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372 .. _v2: https://cancer.sanger.ac.uk/signatures/signatures_v2/
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373 .. _v3.2: https://cancer.sanger.ac.uk/signatures/sbs/
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374
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375 </help>
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376 <citations>
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377 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
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378 <citation type="doi">10.1186/s13073-018-0539-0</citation>
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379 <citation type="doi">10.1038/nature12477</citation>
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380 <citation type="doi">10.1038/s41586-020-1943-3</citation>
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381 </citations>
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382 </tool>