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annotate mutational_patterns.xml @ 24:ca6c19ee7da0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
author artbio
date Tue, 05 Jul 2022 21:41:43 +0000
parents 83f8c93c34b4
children b00fef2b1c2c
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24
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0">
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="3.4.0=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="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
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7 <requirement type="package" version="1.7.1=r41hc72bb7e_0">r-optparse</requirement>
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8 <requirement type="package" version="0.2.21=r41h7525677_1">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>
24
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
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11 <requirement type="package" version="1.4.3=r41hdfd78af_4">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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12 <requirement type="package" version="1.4.4=r41hdfd78af_0">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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34
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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 '$denovo'
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48 --sigmatrix '$sigmatrix'
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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 '$set_preset.signum'
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62 --colors '$set_preset.colors'
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63 --display_signatures '$set_preset.display_signatures'
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64 --output_sigpattern '$sig_contrib'
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65
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66 #if $set_preset.contrib_matrix_out == 'yes'
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67 --sig_contrib_matrix '$sig_contrib_matrix'
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68 #end if
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69
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70 #end if
0
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71
3
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72 #if $rdata_out
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73 --rdata '$rdata'
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74 #end if
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75
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76 --tooldir '$__tool_directory__/'
3
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77
0
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78 ]]></command>
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79 <inputs>
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80 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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81 <param name="genome" type="select" label="Reference Genome">
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82 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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83 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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artbio
parents:
diff changeset
84 </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
85 <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
86 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" 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
87 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
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88 <option value="no" selected="true">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
89 <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
90 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
91 <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
92 <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
93 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
94 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
95 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
96 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
97 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
98 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
99 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
100 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
101 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
102 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
103 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
104 <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
105 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
106 <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
107 <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
108 <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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109 <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
110 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
111 <when value="yes" />
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artbio
parents: 1
diff changeset
112 <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
113 </conditional>
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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114
2
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artbio
parents: 1
diff changeset
115 <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
116 <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
117 <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
diff changeset
118 <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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119 </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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120 <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
121 <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
122 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
123 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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124 <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
125 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
126 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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127 <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
128 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
129 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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130 </when>
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artbio
parents: 1
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131 <when value="no" />
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artbio
parents: 1
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132 </conditional>
0
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133
18
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artbio
parents: 17
diff changeset
134 <conditional name="set_preset">
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artbio
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135 <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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136 <option value="yes" selected="true">Yes</option>
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artbio
parents: 1
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137 <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
138 </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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139 <when value="yes">
18
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artbio
parents: 17
diff changeset
140 <conditional name="set_signature_input">
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artbio
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141 <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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142 <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
143 <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
144 </param>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
145 <when value="cosmic">
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artbio
parents: 17
diff changeset
146 <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
147 <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
148 <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
parents: 17
diff changeset
149 <option value="v3.1">Cosmic v3.1, June 2020</option>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
150 <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
parents: 17
diff changeset
151 </param>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
152 </when>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
153 <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
154 <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
155 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
parents: 17
diff changeset
156 help="see https://cancer.sanger.ac.uk/signatures/documents/453/COSMIC_v3.2_SBS_GRCh38.txt for the required format" />
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
157 </when>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
158 </conditional>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
159 <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
diff changeset
160 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
161 help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
23
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
162 <param name="display_signatures" type="select" display="radio" label="Output profiles of input signatures ?">
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
163 <option value="no">No</option>
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
164 <option value="yes" selected="true">Yes</option>
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
165 </param>
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
166 <param name="contrib_matrix_out" type="select" display="radio" label="Output Signature Contribution table ?"
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
167 help="Output the normalized signatures contributions for further visualization" >
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artbio
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168 <option value="no" selected="true">No</option>
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artbio
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169 <option value="yes">Yes</option>
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170 </param>
20
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artbio
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171 <param name="colors" type="select" label="Color set" display="radio">
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artbio
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172 <option value="brewer">RColorBrewer</option>
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artbio
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173 <option value="intense" selected="true">Intense</option>
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artbio
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174 </param>
2
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artbio
parents: 1
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175 </when>
18
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artbio
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176 <when value="no" />
3
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artbio
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177 </conditional>
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artbio
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178 <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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179 </inputs>
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180 <outputs>
2
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artbio
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181 <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
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182 <filter>set_spectrum['choices'] == "yes"</filter>
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artbio
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183 </data>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
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184 <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
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185 <filter>set_denovo['choices'] == "yes"</filter>
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artbio
parents: 1
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186 </data>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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187 <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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188 <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
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diff changeset
189 </data>
18
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artbio
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diff changeset
190 <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
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191 <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
192 </data>
11
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artbio
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diff changeset
193 <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
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194 <filter>set_preset['choices'] == "yes" and set_preset['contrib_matrix_out'] == "yes"</filter>
11
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artbio
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195 </data>
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196
3
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artbio
parents: 2
diff changeset
197 <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
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198 <filter>rdata_out</filter>
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artbio
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diff changeset
199 </data>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
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200
0
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artbio
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diff changeset
201 </outputs>
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artbio
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diff changeset
202 <tests>
24
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artbio
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diff changeset
203 <!-- de novo signatures -->
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artbio
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204 <test>
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artbio
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diff changeset
205 <param name="vcfs">
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artbio
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diff changeset
206 <collection type="list">
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artbio
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diff changeset
207 <element name="6" value="F.vcf"/>
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artbio
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diff changeset
208 <element name="7" value="G.vcf"/>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
209 <element name="8" value="H.vcf"/>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
210 <element name="9" value="I.vcf"/>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
211 </collection>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
212 </param>
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artbio
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213 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
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artbio
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diff changeset
214 <conditional name="set_spectrum">
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artbio
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diff changeset
215 <param name="choices" value="no"/>
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artbio
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diff changeset
216 </conditional>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
217 <conditional name="set_denovo">
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
218 <param name="choices" value="yes"/>
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219 </conditional>
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artbio
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diff changeset
220 <conditional name="set_preset">
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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221 <param name="choices" value="no"/>
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artbio
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222 </conditional>
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artbio
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diff changeset
223 <param name="nrun" value="10" />
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
224 <param name="rank" value="4" />
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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225 <param name="newsignum" value="4" />
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artbio
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226 <param name="rdata_out" value="true" />
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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diff changeset
227 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
artbio
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228 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
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artbio
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229 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
ca6c19ee7da0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit bad92e3210a78b5ebf47d6950f4dba10c1cbf07d
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230 </test>
23
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
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diff changeset
231 <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
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232 <test>
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233 <param name="vcfs">
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artbio
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234 <collection type="list">
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artbio
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235 <element name="6" value="F.vcf"/>
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artbio
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236 <element name="7" value="G.vcf"/>
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artbio
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237 <element name="8" value="H.vcf"/>
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artbio
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238 <element name="9" value="I.vcf"/>
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239 </collection>
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diff changeset
240 </param>
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241 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
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artbio
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242 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
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artbio
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diff changeset
243 <conditional name="set_spectrum">
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artbio
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244 <param name="choices" value="no"/>
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245 </conditional>
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artbio
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246 <conditional name="set_denovo">
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artbio
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247 <param name="choices" value="no"/>
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248 </conditional>
18
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artbio
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diff changeset
249 <conditional name="set_preset">
15
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250 <param name="choices" value="yes"/>
18
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artbio
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diff changeset
251 <conditional name="set_signature_input">
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diff changeset
252 <param name="input_signature_choices" value="user_signatures" />
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diff changeset
253 <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
254 </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
255 <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
256 </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
257 <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
258 <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
259 <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
260 </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
261 <!-- 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
262 <test>
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="vcfs">
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
264 <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
265 <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
266 <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
267 <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
268 <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
269 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
270 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
271 <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
272 <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
273 <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
274 <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
275 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
276 <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
277 <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
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 <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
280 <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
281 <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
282 <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
283 <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
284 </conditional>
23
83f8c93c34b4 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
artbio
parents: 22
diff changeset
285 <param name="display_signatures" value="no" />
15
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
286 <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
287 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
288 <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
289 <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
290 <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
291 </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
292 <!-- 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
293 <test>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
294 <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
295 <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
296 <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
297 <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
298 <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
299 <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
300 </collection>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
301 </param>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
302 <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
303 <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
304 <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
305 <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
306 </conditional>
8182d1625433 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
artbio
parents: 14
diff changeset
307 <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
308 <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
309 </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
310 <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
311 <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
312 <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
313 <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
314 <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
315 </conditional>
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
artbio
parents: 17
diff changeset
316 <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
317 </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
318 <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
319 <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
320 <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
321 </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
322 <!-- 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
323 <test>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
324 <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
325 <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
326 <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
327 <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
328 </collection>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
329 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
330 <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
331 <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
332 <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
333 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
334 <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
335 <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
336 <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
337 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
338 <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
339 <param name="choices" value="no"/>
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340 </conditional>
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341 <conditional name="set_preset">
2
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342 <param name="choices" value="no"/>
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343 </conditional>
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344 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
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345 </test>
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346 </tests>
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347 <help>
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348
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349 **What it does**
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350
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351 This tool implement the R package MutationalPatterns to decompose mutations found in cancers
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352 in a linear combination of elementary mutational signatures, as first described by
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
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353 Alexandrov_ et al (2013) and recently improved in an update_ published in 2020.
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354
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355 .. _Alexandrov: https://www.nature.com/articles/nature12477
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356 .. _update: https://www.nature.com/articles/s41586-020-1943-3
0
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357
18
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358 Sets of elementary signatures found by analyzing large cohortes of patients are published
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359 in the COSMIC databases v2_ to v3.2_. You can choose among these COSMIC signature sets to
8d9f31389f33 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 1cb9c8fd0c74943a8e6de4c63ac5e4a84ef27430"
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360 analyse your own VCFs.
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361
18
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362 In addition, you can use your own signature sets (or filtered COSMIC signature sets)
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363 since MutationalPatterns implements a method to extract elementary signatures from
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364 user-provided VCFs.
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365
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366 **Inputs**
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367
18
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368 * a collection of VCF files with somatic mutations calls from analysis of samples.
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369 * a tabular table describing the correspondance of sample names to levels of a factor
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370 (tissues, ages, sexes, etc.)
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371
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372 **Outputs**
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373
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374 This tool returns pdf files with various visualisations of :
0
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375
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376 * the spectrum of single nucleotide mutation types
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377 * the absolute contribution of the elementary signatures in the samples
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378 * the relative contribution of the elementary signatures in the samples
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379 * an unrooted hierarchical clustering of the reconstructed samples with respect to the relative contribution of elementary signatures
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380 * the Cosine similarity between true samples and samples reconstructed with elementary signatures
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381 * pie charts displaying the relative contribution of the n most contributing elementary signatures in the reconstructed sample profiles
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382
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383 .. _v2: https://cancer.sanger.ac.uk/signatures/signatures_v2/
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384 .. _v3.2: https://cancer.sanger.ac.uk/signatures/sbs/
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385
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386 </help>
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387 <citations>
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388 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
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389 <citation type="doi">10.1186/s13073-018-0539-0</citation>
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390 <citation type="doi">10.1038/nature12477</citation>
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391 <citation type="doi">10.1038/s41586-020-1943-3</citation>
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392 </citations>
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393 </tool>