Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.xml @ 14:56c8869a231e draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
author artbio
date Fri, 04 Jun 2021 22:35:48 +0000
parents 6741b819cc15
children 8182d1625433
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13:6741b819cc15 14:56c8869a231e
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy13.1"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14">
2 <description>from genomic variations in vcf files</description> 2 <description>from genomic variations in vcf files</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> 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> 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> 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> 7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> 8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
9 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
9 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> 10 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
11 <!--
12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
10 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement> 13 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
11 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> 14 -->
12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement> 15 <!--
13 <!-- install bioconda genomes 16 install more bioconda genomes
14 bioconductor-bsgenome.mmusculus.ucsc.mm9 17 bioconductor-bsgenome.mmusculus.ucsc.mm9
15 bioconductor-bsgenome.mmusculus.ucsc.mm10 --> 18 bioconductor-bsgenome.mmusculus.ucsc.mm10
19 -->
16 </requirements> 20 </requirements>
17 <stdio> 21 <stdio>
18 <exit_code range="1:" level="fatal" description="Tool exception" /> 22 <exit_code range="1:" level="fatal" description="Tool exception" />
19 </stdio> 23 </stdio>
20 24
21 <command detect_errors="exit_code"><![CDATA[ 25 <command detect_errors="exit_code"><![CDATA[
22 #import json 26 #import json
23 #import os 27 #import os
24 Rscript $__tool_directory__/mutational_patterns.R 28 Rscript $__tool_directory__/mutational_patterns.R
25 --inputs 29 --inputs
26 #set $filename_to_element_identifiers = {} 30 #set $filename_to_element_identifiers = {}
61 65
62 ]]></command> 66 ]]></command>
63 <inputs> 67 <inputs>
64 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> 68 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
65 <param name="genome" type="select" label="Reference Genome"> 69 <param name="genome" type="select" label="Reference Genome">
66 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> 70 <!-- <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> -->
67 <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option> 71 <!-- <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option> -->
68 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option> 72 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
69 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option> 73 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
70 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option> 74 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
71 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>--> 75 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
72 </param> 76 </param>
278 282
279 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_ 283 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_
280 * 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) 284 * 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)
281 * 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) 285 * 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)
282 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures 286 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures
283 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern 287 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures to their mutational pattern
284 288
285 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt 289 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt
286 290
287 </help> 291 </help>
288 <citations> 292 <citations>