Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.xml @ 0:924c527fb379 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e1f3ca871f13569401f41a5af9d0e281bf372540"
author artbio
date Sun, 13 Sep 2020 18:40:29 +0000
parents
children 921c1f55481d
comparison
equal deleted inserted replaced
-1:000000000000 0:924c527fb379
1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_1">
2 <description>from genomic variations in vcf files</description>
3 <requirements>
4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
8 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
9 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
10 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
11 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
12 <!-- install bioconda genomes
13 bioconductor-bsgenome.mmusculus.ucsc.mm9
14 bioconductor-bsgenome.mmusculus.ucsc.mm10 -->
15 </requirements>
16 <stdio>
17 <exit_code range="1:" level="fatal" description="Tool exception" />
18 </stdio>
19
20 <command detect_errors="exit_code"><![CDATA[
21 #import json
22 #import os
23 Rscript $__tool_directory__/mutational_patterns.R
24 --inputs
25 #set $filename_to_element_identifiers = {}
26 #for $sample in $vcfs:
27 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
28 #end for
29 '#echo json.dumps(filename_to_element_identifiers)#'
30 --genome '$genome'
31 --levels '$levels'
32 --signum '$signum'
33 --output '$output'
34
35 ]]></command>
36 <inputs>
37 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
38 <param name="genome" type="select" label="Reference Genome">
39 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>
40 <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option>
41 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
42 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
43 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
44 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
45 </param>
46 <param name="levels" type="data" format="tabular"
47 label="A two-column tab-separated file describing levels attributed to each sample name"
48 help="Tip: the sample name list in the vcf collection can be obtained using
49 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
50 example:&lt;br&gt;
51 sample1 female&lt;br&gt;
52 sample2 female&lt;br&gt;
53 sample3 male&lt;br&gt;
54 sample4 female&lt;br&gt;
55 sample5 male&lt;br&gt;
56 sample5 male" />
57 <param name="signum" type="integer" value="2" min="2" max="30"
58 label="selects the N most significant signatures in samples to express mutational patterns"
59 help="an integer between 2 and 30 signature types from cosmic"/>
60
61 </inputs>
62 <outputs>
63 <data name="output" format="pdf" label="Mutational Patterns/Signatures" />
64 </outputs>
65 <tests>
66 <test>
67 <param name="vcfs">
68 <collection type="list">
69 <element name="1" value="EGF167.vcf"/>
70 <element name="2" value="EGF089.vcf"/>
71 <element name="3" value="EGF037F.vcf"/>
72 </collection>
73 </param>
74 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
75 <param name="levels" value="levels.tab" ftype="tabular"/>
76 <param name="signum" value="3" />
77 <output name="output" file="output.pdf" compare="sim_size" ftype="pdf"/>
78 </test>
79 </tests>
80 <help>
81
82 **What it does**
83
84 Takes as inputs
85
86 * a collection of n vcf files corresponding to n samples.
87 * a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.)
88 * the number of cosmic signatures to decompose mutational patterns of samples
89
90
91 This tool returns a pdf file with the visualisation :
92
93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic
94 * 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)
95 * 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)
96 * a clustering of the samples with respect to the relative contribution of their cosmic signatures
97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic signatures in their mutational pattern
98
99
100 </help>
101 <citations>
102 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation>
103 <citation type="doi">10.1186/s13073-018-0539-0</citation>
104 <citation type="doi">10.1038/nature12477</citation>
105 </citations>
106 </tool>