Mercurial > repos > artbio > mutational_patterns
diff mutational_patterns.xml @ 3:e332cf9dfa06 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
author | artbio |
---|---|
date | Thu, 24 Sep 2020 01:32:52 +0000 |
parents | aea952be68cb |
children | 7ba08c826888 |
line wrap: on
line diff
--- a/mutational_patterns.xml Wed Sep 16 22:58:28 2020 +0000 +++ b/mutational_patterns.xml Thu Sep 24 01:32:52 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0+galaxy3"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy4"> <description>from genomic variations in vcf files</description> <requirements> <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> @@ -43,13 +43,19 @@ --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 #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"/> @@ -90,6 +96,7 @@ <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> @@ -101,10 +108,10 @@ 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"/> + 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"/> + 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> @@ -118,9 +125,14 @@ <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> </when> <when value="no" /> - </conditional> + </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"> @@ -129,53 +141,19 @@ <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="rdata" format="rdata" label="${tool.name}: RData file"> + <filter>rdata_out</filter> + </data> + </outputs> <tests> - <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"/> - <param name="levels" value="GH_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"/> - </conditional> - <param name="signum" value="3" /> - <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> - </test> - <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> - <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/> - </test> + <!-- simple profile --> <test> <param name="vcfs"> <collection type="list"> @@ -199,6 +177,60 @@ </conditional> <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/> </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" ftype="pdf"/> + <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" 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="GH_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"/> + </conditional> + <param name="signum" value="3" /> + <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> + </test> </tests> <help>