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annotate mutational_patterns.xml @ 17:8c6ee1c2248f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"
author artbio
date Tue, 05 Oct 2021 22:28:34 +0000
parents 31e7a33ecd71
children 8d9f31389f33
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy2">
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="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
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6 <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
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7 <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
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8 <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
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9 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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10 <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
14
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11 <!--
0
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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 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
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14 -->
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15 <!--
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16 install more bioconda genomes
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17 bioconductor-bsgenome.mmusculus.ucsc.mm9
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18 bioconductor-bsgenome.mmusculus.ucsc.mm10
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19 -->
0
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20 </requirements>
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21 <stdio>
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22 <exit_code range="1:" level="fatal" description="Tool exception" />
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23 </stdio>
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24
14
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25 <command detect_errors="exit_code"><![CDATA[
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26 #import json
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27 #import os
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28 Rscript $__tool_directory__/mutational_patterns.R
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29 --inputs
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30 #set $filename_to_element_identifiers = {}
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31 #for $sample in $vcfs:
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32 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
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33 #end for
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34 '#echo json.dumps(filename_to_element_identifiers)#'
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35 --genome '$genome'
2
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36
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37 #if $set_levels.choices == 'yes':
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38 --levels '$set_levels.levels'
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39 #end if
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41 #if $set_spectrum.choices == 'yes':
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42 --output_spectrum $spectrum
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43 #end if
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44
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45 #if $set_denovo.choices == 'yes':
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46 --nrun $set_denovo.nrun
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47 --rank $set_denovo.rank
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48 --newsignum $set_denovo.newsignum
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49 --output_denovo $denovo
3
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50 --sigmatrix $sigmatrix
2
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51 #end if
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52
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53 #if $set_cosmic.choices == 'yes':
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54 --cosmic_version '$set_cosmic.cosmic_version'
2
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55 --signum '$set_cosmic.signum'
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56 --output_cosmic $cosmic
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57 #if $set_cosmic.contrib_matrix_out == 'yes'
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58 --sig_contrib_matrix $sig_contrib_matrix
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59 #end if
2
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60 #end if
0
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61
3
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62 #if $rdata_out
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63 --rdata '$rdata'
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64 #end if
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65
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66 --tooldir '$__tool_directory__/'
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67
0
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68 ]]></command>
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69 <inputs>
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70 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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71 <param name="genome" type="select" label="Reference Genome">
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72 <!-- <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> -->
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73 <!-- <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option> -->
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74 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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75 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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76 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
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77 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
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78 </param>
2
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79 <conditional name="set_levels">
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80 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
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81 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
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82 <option value="no" selected="true">No</option>
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83 <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
84 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
85 <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
86 <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
87 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
88 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
89 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
90 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
91 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
92 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
93 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
94 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
95 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
96 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
97 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
98 <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
99 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
100 <conditional name="set_spectrum">
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artbio
parents: 1
diff changeset
101 <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
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102 <option value="yes" selected="true">Yes</option>
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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103 <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
104 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
105 <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
106 <when value="no" />
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artbio
parents: 1
diff changeset
107 </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
108
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
109 <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
110 <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"
artbio
parents: 1
diff changeset
111 <option value="yes" selected="true">Yes</option>
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artbio
parents: 1
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112 <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
113 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
114 <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
115 <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
diff changeset
116 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
117 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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118 <param name="rank" type="integer" value="4" min="3" 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
119 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
120 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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121 <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
122 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
123 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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124 </when>
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artbio
parents: 1
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125 <when value="no" />
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artbio
parents: 1
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126 </conditional>
0
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127
2
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artbio
parents: 1
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128 <conditional name="set_cosmic">
15
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artbio
parents: 14
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129 <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio">
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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parents: 1
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130 <option value="yes" selected="true">Yes</option>
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artbio
parents: 1
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131 <option value="no">No</option>
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artbio
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132 </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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133 <when value="yes">
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artbio
parents: 1
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134 <param name="signum" type="integer" value="3" 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
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135 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
parents: 1
diff changeset
136 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"
artbio
parents: 2
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137 <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"
artbio
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138 <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"
artbio
parents: 2
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139 <option value="v3">Cosmic v3, May 2019</option>
17
8c6ee1c2248f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"
artbio
parents: 16
diff changeset
140 <option value="v3.1">Cosmic v3.1, June 2020</option>
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artbio
parents: 16
diff changeset
141 <option value="v3.2">Cosmic v3.2, March 2021</option>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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142 </param>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
143 <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
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144 help="Output the normalized signatures contributions for further visualization" >
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artbio
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145 <option value="no" selected="true">No</option>
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artbio
parents: 14
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146 <option value="yes">Yes</option>
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147 </param>
2
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artbio
parents: 1
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148 </when>
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artbio
parents: 1
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149 <when value="no" />
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
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150 </conditional>
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artbio
parents: 2
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151 <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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152 </inputs>
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153 <outputs>
2
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parents: 1
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154 <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
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155 <filter>set_spectrum['choices'] == "yes"</filter>
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artbio
parents: 1
diff changeset
156 </data>
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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157 <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
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158 <filter>set_denovo['choices'] == "yes"</filter>
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artbio
parents: 1
diff changeset
159 </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
160 <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
161 <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
162 </data>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
163 <data name="cosmic" format="pdf" label="Cosmic signatures">
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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164 <filter>set_cosmic['choices'] == "yes"</filter>
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artbio
parents: 1
diff changeset
165 </data>
11
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artbio
parents: 10
diff changeset
166 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
15
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parents: 14
diff changeset
167 <filter>set_cosmic['choices'] == "yes" and set_cosmic['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
168 </data>
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diff changeset
169
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
170 <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
171 <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
172 </data>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
173
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
174 </outputs>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
175 <tests>
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
176 <!-- cosmic signatures with cosmic V3 -->
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
177 <test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
185 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
186 <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
187 <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
188 <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
189 <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
190 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
191 <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
192 <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
193 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
194 <conditional name="set_cosmic">
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="choices" 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
196 <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
197 <param name="cosmic_version" value="v3"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
198 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
199 <param name="signum" value="3" />
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
200 <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
201 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
202 </test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
203
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
204 <!-- cosmic signatures -->
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
205 <test>
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="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
207 <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
208 <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
209 <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
210 <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
211 <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
212 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
213 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
214 <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
215 <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
216 <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
217 <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
218 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
219 <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
220 <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
221 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
222 <conditional name="set_cosmic">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
223 <param name="choices" 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
224 <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
225 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
226 <param name="signum" value="3" />
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
227 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
228 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
229 </test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
230
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
231 <!-- cosmic signature on single sample -->
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
232 <test>
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="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
234 <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
235 <element name="1" 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
236 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
237 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
238 <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
239 <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
240 <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
241 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
242 <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
243 <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
244 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
245 <conditional name="set_cosmic">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
246 <param name="choices" 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
247 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
248 <param name="signum" value="5" />
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
249 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
250 </test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
251
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
252 <!-- simple profile -->
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
253 <test>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
254 <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
255 <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
256 <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
257 <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
258 </collection>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
259 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
260 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
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261 <conditional name="set_levels">
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262 <param name="choices" value="yes"/>
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263 </conditional>
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264 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
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265 <conditional name="set_spectrum">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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266 <param name="choices" value="yes"/>
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267 </conditional>
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268 <conditional name="set_denovo">
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artbio
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269 <param name="choices" value="no"/>
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270 </conditional>
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271 <conditional name="set_cosmic">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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272 <param name="choices" value="no"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
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273 </conditional>
11
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274 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
0
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275 </test>
3
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276
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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277 <!-- de novo signatures -->
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278 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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279 <param name="vcfs">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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280 <collection type="list">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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281 <element name="6" value="F.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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282 <element name="7" value="G.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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283 <element name="8" value="H.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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284 <element name="9" value="I.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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285 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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286 </param>
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artbio
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287 <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"
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288 <conditional name="set_spectrum">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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289 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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290 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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291 <conditional name="set_denovo">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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292 <param name="choices" value="yes"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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293 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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294 <conditional name="set_cosmic">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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295 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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296 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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297 <param name="nrun" value="10" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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298 <param name="rank" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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299 <param name="newsignum" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
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300 <param name="rdata_out" value="true" />
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301 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
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302 <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"
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303 <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"
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304 </test>
0
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305 </tests>
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306 <help>
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307
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308 **What it does**
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309
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310 Takes as inputs
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311
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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312 * a collection of n vcf files corresponding to n samples.
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313 * a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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314 * the number of cosmic signatures to decompose mutational patterns of samples
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315
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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316
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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317 This tool returns a pdf file with the visualisation :
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318
1
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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319 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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320 * the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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321 * the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30)
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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322 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
14
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323 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures to their mutational pattern
0
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324
1
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325 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
0
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326
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327 </help>
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328 <citations>
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329 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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330 <citation type="doi">10.1186/s13073-018-0539-0</citation>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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331 <citation type="doi">10.1038/nature12477</citation>
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332 </citations>
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333 </tool>