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annotate mutational_patterns.xml @ 10:59c0e2a7965c draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 533394bd219d56cde7fb9721803e8aed8fd5a25d"
author artbio
date Mon, 19 Oct 2020 23:34:58 +0000
parents 4ff3c984523b
children 7995a949189f
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy11">
0
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2 <description>from genomic variations in vcf files</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
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5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
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6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
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7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
2
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8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
0
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9 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
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10 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
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11 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
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12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
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13 <!-- install bioconda genomes
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14 bioconductor-bsgenome.mmusculus.ucsc.mm9
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15 bioconductor-bsgenome.mmusculus.ucsc.mm10 -->
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16 </requirements>
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17 <stdio>
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18 <exit_code range="1:" level="fatal" description="Tool exception" />
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19 </stdio>
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21 <command detect_errors="exit_code"><![CDATA[
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22 #import json
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23 #import os
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24 Rscript $__tool_directory__/mutational_patterns.R
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25 --inputs
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26 #set $filename_to_element_identifiers = {}
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27 #for $sample in $vcfs:
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28 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
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29 #end for
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30 '#echo json.dumps(filename_to_element_identifiers)#'
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31 --genome '$genome'
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32
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33 #if $set_levels.choices == 'yes':
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34 --levels '$set_levels.levels'
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35 #end if
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36
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37 #if $set_spectrum.choices == 'yes':
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38 --output_spectrum $spectrum
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39 #end if
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40
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41 #if $set_denovo.choices == 'yes':
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42 --nrun $set_denovo.nrun
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43 --rank $set_denovo.rank
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44 --newsignum $set_denovo.newsignum
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45 --output_denovo $denovo
3
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46 --sigmatrix $sigmatrix
2
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47 #end if
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48
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49 #if $set_cosmic.choices == 'yes':
3
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50 --cosmic_version $set_cosmic.cosmic_version
2
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51 --signum '$set_cosmic.signum'
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52 --output_cosmic $cosmic
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53 #end if
0
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54
3
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55 #if $rdata_out
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56 --rdata '$rdata'
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57 #end if
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58
0
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59 ]]></command>
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60 <inputs>
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61 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
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62 <param name="genome" type="select" label="Reference Genome">
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63 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>
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64 <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option>
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65 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
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66 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
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67 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
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68 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
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69 </param>
2
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70 <conditional name="set_levels">
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71 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
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72 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
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73 <option value="no" selected="true">No</option>
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74 <option value="yes">Yes</option>
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75 </param>
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76 <when value="yes">
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77 <param name="levels" type="data" format="tabular"
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78 label="A two-column tab-separated file describing levels attributed to each sample name"
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79 help="Tip: the sample name list in the vcf collection can be obtained using
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80 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
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81 example:&lt;br&gt;
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82 sample1 female&lt;br&gt;
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83 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
84 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
85 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
86 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
87 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
88 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
89 <when value="no" />
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
90 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
91 <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
92 <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
93 <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
diff changeset
94 <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
95 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
96 <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
97 <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
98 </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
99
2
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_denovo">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
101 <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
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
diff changeset
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 <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
107 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
108 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
diff changeset
109 <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
110 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
111 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
diff changeset
112 <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
113 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
114 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
diff changeset
115 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
116 <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
117 </conditional>
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
118
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
119 <conditional name="set_cosmic">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
120 <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
121 <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
diff changeset
122 <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
123 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
124 <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
125 <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
126 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
127 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
diff changeset
128 <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
parents: 2
diff changeset
129 <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
diff changeset
130 <option value="v3">Cosmic v3, May 2019</option>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
131 </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
132 </when>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
133 <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
diff changeset
134 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
135 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
136 </inputs>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
137 <outputs>
2
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
138 <data name="spectrum" format="pdf" label="Mutational Spectrum">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
139 <filter>set_spectrum['choices'] == "yes"</filter>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
140 </data>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
141 <data name="denovo" format="pdf" label="De novo signatures">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
142 <filter>set_denovo['choices'] == "yes"</filter>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
143 </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
144 <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
145 <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
146 </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
147 <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
diff changeset
148 <filter>set_cosmic['choices'] == "yes"</filter>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
149 </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
150 <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
151 <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
152 </data>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
153
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
154 </outputs>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
155 <tests>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
156 <!-- 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
157 <test>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
158 <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
159 <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
160 <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
161 <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
162 </collection>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
163 </param>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
164 <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
165 <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
166 <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
167 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
168 <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
169 <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
170 <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
171 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
172 <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
173 <param name="choices" value="no"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
174 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
175 <conditional name="set_cosmic">
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
176 <param name="choices" value="no"/>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
177 </conditional>
aea952be68cb "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
artbio
parents: 1
diff changeset
178 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
179 </test>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
180
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
181 <!-- de novo signatures -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
182 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
183 <param name="vcfs">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
184 <collection type="list">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
185 <element name="6" value="F.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
186 <element name="7" value="G.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
187 <element name="8" value="H.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
188 <element name="9" value="I.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
189 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
190 </param>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
191 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
192 <conditional name="set_spectrum">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
193 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
194 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
195 <conditional name="set_denovo">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
196 <param name="choices" value="yes"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
197 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
198 <conditional name="set_cosmic">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
199 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
200 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
201 <param name="nrun" value="10" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
202 <param name="rank" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
203 <param name="newsignum" value="4" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
204 <param name="rdata_out" value="true" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
205 <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
206 <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" compare="sim_size"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
207 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
208 </test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
209
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
210 <!-- cosmic signatures -->
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
211 <test>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
212 <param name="vcfs">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
213 <collection type="list">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
214 <element name="6" value="F.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
215 <element name="7" value="G.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
216 <element name="8" value="H.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
217 <element name="9" value="I.vcf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
218 </collection>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
219 </param>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
220 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
4
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
221 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
3
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
222 <conditional name="set_spectrum">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
223 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
224 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
225 <conditional name="set_denovo">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
226 <param name="choices" value="no"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
227 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
228 <conditional name="set_cosmic">
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
229 <param name="choices" value="yes"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
230 </conditional>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
231 <param name="signum" value="3" />
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
232 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
e332cf9dfa06 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
artbio
parents: 2
diff changeset
233 </test>
8
e0dad46148bf "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
artbio
parents: 7
diff changeset
234 <!-- cosmic signature on single sample -->
4
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
235 <test>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
236 <param name="vcfs">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
237 <collection type="list">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
238 <element name="1" value="G.vcf"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
239 </collection>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
240 </param>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
241 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
242 <conditional name="set_spectrum">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
243 <param name="choices" value="no"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
244 </conditional>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
245 <conditional name="set_denovo">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
246 <param name="choices" value="no"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
247 </conditional>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
248 <conditional name="set_cosmic">
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
249 <param name="choices" value="yes"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
250 </conditional>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
251 <param name="signum" value="5" />
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
252 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000" ftype="pdf"/>
7ba08c826888 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
artbio
parents: 3
diff changeset
253 </test>
0
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
254 </tests>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
255 <help>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
256
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
diff changeset
257 **What it does**
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
artbio
parents:
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258
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259 Takes as inputs
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260
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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261 * a collection of n vcf files corresponding to n samples.
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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262 * 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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263 * the number of cosmic signatures to decompose mutational patterns of samples
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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264
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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265
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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266 This tool returns a pdf file with the visualisation :
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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267
1
921c1f55481d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
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268 * 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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269 * 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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270 * 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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271 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
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272 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern
0
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273
1
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274 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
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275
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276 </help>
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277 <citations>
924c527fb379 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
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278 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
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279 <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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280 <citation type="doi">10.1038/nature12477</citation>
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281 </citations>
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282 </tool>