Mercurial > repos > artbio > mutational_patterns
diff mutational_patterns.xml @ 0:d585f369bfad draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"
| author | artbio |
|---|---|
| date | Fri, 04 Jun 2021 22:35:17 +0000 |
| parents | |
| children | c73aa7cc4c4b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutational_patterns.xml Fri Jun 04 22:35:17 2021 +0000 @@ -0,0 +1,297 @@ +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14"> + <description>from genomic variations in vcf files</description> + <requirements> + <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> + <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> + <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement> + <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement> + <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> + <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> + <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> +<!-- + <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement> + <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement> +--> +<!-- +install more bioconda genomes +bioconductor-bsgenome.mmusculus.ucsc.mm9 +bioconductor-bsgenome.mmusculus.ucsc.mm10 +--> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + + <command detect_errors="exit_code"><![CDATA[ +#import json +#import os +Rscript $__tool_directory__/mutational_patterns.R + --inputs + #set $filename_to_element_identifiers = {} + #for $sample in $vcfs: + $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier) + #end for + '#echo json.dumps(filename_to_element_identifiers)#' + --genome '$genome' + + #if $set_levels.choices == 'yes': + --levels '$set_levels.levels' + #end if + + #if $set_spectrum.choices == 'yes': + --output_spectrum $spectrum + #end if + + #if $set_denovo.choices == 'yes': + --nrun $set_denovo.nrun + --rank $set_denovo.rank + --newsignum $set_denovo.newsignum + --output_denovo $denovo + --sigmatrix $sigmatrix + #end if + + #if $set_cosmic.choices == 'yes': + --cosmic_version '$set_cosmic.cosmic_version' + --signum '$set_cosmic.signum' + --output_cosmic $cosmic + #if $set_cosmic.contrib_matrix_out + --sig_contrib_matrix $sig_contrib_matrix + #end if + #end if + + #if $rdata_out + --rdata '$rdata' + #end if + +]]></command> + <inputs> + <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> + <param name="genome" type="select" label="Reference Genome"> + <!-- <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> --> + <!-- <option value="BSgenome.Hsapiens.NCBI.GRCh38">BSgenome.Hsapiens.NCBI.GRCh38</option> --> + <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option> + <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option> + <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option> + <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>--> + </param> + <conditional name="set_levels"> + <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio" + help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc."> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="levels" type="data" format="tabular" + label="A two-column tab-separated file describing levels attributed to each sample name" + help="Tip: the sample name list in the vcf collection can be obtained using + the IUC Galaxy tool 'Extract element identifiers of a list collection' <br> + example:<br> + sample1 female<br> + sample2 female<br> + sample3 male<br> + sample4 female<br> + sample5 male<br> + sample5 male" /> + </when> + <when value="no" /> + </conditional> + <conditional name="set_spectrum"> + <param name="choices" type="select" label="Analyse Mutational Spectrum" display="radio"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes" /> + <when value="no" /> + </conditional> + + <conditional name="set_denovo"> + <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="nrun" type="integer" value="10" min="10" max="200" + label="Number of cycles to find best fitting of signatures" + help="High values extend the computational time"/> + <param name="rank" type="integer" value="4" min="3" max="30" + label="Number of ranks to be displayed for control of optimal number of signature" + 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"/> + <param name="newsignum" type="integer" value="4" min="2" max="30" + label="Number of de novo signatures to capture" + help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/> + </when> + <when value="no" /> + </conditional> + + <conditional name="set_cosmic"> + <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="signum" type="integer" value="3" min="2" max="30" + label="selects the N most significant signatures in samples to express mutational patterns" + help="an integer between 2 and 30 signature types from cosmic"/> + <param name="cosmic_version" type="select" label="Version of the Cosmic signature set"> + <option value="v2" selected="true">Cosmic v2, March 2015</option> + <option value="v3">Cosmic v3, May 2019</option> + </param> + <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?" + help="Output the normalized signatures contributions for further visualization" /> + </when> + <when value="no" /> + </conditional> + <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" /> + </inputs> + <outputs> + <data name="spectrum" format="pdf" label="Mutational Spectrum"> + <filter>set_spectrum['choices'] == "yes"</filter> + </data> + <data name="denovo" format="pdf" label="De novo signatures"> + <filter>set_denovo['choices'] == "yes"</filter> + </data> + <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix"> + <filter>set_denovo['choices'] == "yes"</filter> + </data> + <data name="cosmic" format="pdf" label="Cosmic signatures"> + <filter>set_cosmic['choices'] == "yes"</filter> + </data> + <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table"> + <filter>set_cosmic['contrib_matrix_out']</filter> + </data> + + <data name="rdata" format="rdata" label="${tool.name}: RData file"> + <filter>rdata_out</filter> + </data> + + </outputs> + <tests> + <!-- simple profile --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="1" ftype="vcf" value="G.vcf"/> + <element name="2" ftype="vcf" value="H.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <conditional name="set_levels"> + <param name="choices" value="yes"/> + </conditional> + <param name="levels" value="GH_levels.tab" ftype="tabular"/> + <conditional name="set_spectrum"> + <param name="choices" value="yes"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="no"/> + </conditional> + <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/> + </test> + + <!-- de novo signatures --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="6" value="F.vcf"/> + <element name="7" value="G.vcf"/> + <element name="8" value="H.vcf"/> + <element name="9" value="I.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="yes"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="no"/> + </conditional> + <param name="nrun" value="10" /> + <param name="rank" value="4" /> + <param name="newsignum" value="4" /> + <param name="rdata_out" value="true" /> + <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/> + <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/> + <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" --> + </test> + + <!-- cosmic signatures --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="6" value="F.vcf"/> + <element name="7" value="G.vcf"/> + <element name="8" value="H.vcf"/> + <element name="9" value="I.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <param name="levels" value="FGHI_levels.tab" ftype="tabular"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="yes"/> + <param name="contrib_matrix_out" value="true" /> + </conditional> + <param name="signum" value="3" /> + <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/> + <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/> + </test> + <!-- cosmic signature on single sample --> + <test> + <param name="vcfs"> + <collection type="list"> + <element name="1" value="G.vcf"/> + </collection> + </param> + <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> + <conditional name="set_spectrum"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_denovo"> + <param name="choices" value="no"/> + </conditional> + <conditional name="set_cosmic"> + <param name="choices" value="yes"/> + </conditional> + <param name="signum" value="5" /> + <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/> + </test> + </tests> + <help> + +**What it does** + +Takes as inputs + +* a collection of n vcf files corresponding to n samples. +* a tabular table describing the correspondance of sample names to levels (tissues, ages, sexes, etc.) +* the number of cosmic signatures to decompose mutational patterns of samples + + +This tool returns a pdf file with the visualisation : + +* the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_ +* 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) +* 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) +* a clustering of the samples with respect to the relative contribution of their cosmic_ signatures +* pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures to their mutational pattern + +.. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt + + </help> + <citations> + <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation> + <citation type="doi">10.1186/s13073-018-0539-0</citation> + <citation type="doi">10.1038/nature12477</citation> + </citations> +</tool>