Mercurial > repos > artbio > mutational_patterns
diff mutational_patterns.xml @ 15:8182d1625433 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
author | artbio |
---|---|
date | Sun, 03 Oct 2021 09:29:04 +0000 |
parents | 56c8869a231e |
children | 31e7a33ecd71 |
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--- a/mutational_patterns.xml Fri Jun 04 22:35:48 2021 +0000 +++ b/mutational_patterns.xml Sun Oct 03 09:29:04 2021 +0000 @@ -1,13 +1,13 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0"> <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="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> + <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement> + <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement> + <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement> + <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement> + <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> + <requirement type="package" version="1.4.3=r41hdfd78af_3">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> @@ -54,7 +54,7 @@ --cosmic_version '$set_cosmic.cosmic_version' --signum '$set_cosmic.signum' --output_cosmic $cosmic - #if $set_cosmic.contrib_matrix_out + #if $set_cosmic.contrib_matrix_out == 'yes' --sig_contrib_matrix $sig_contrib_matrix #end if #end if @@ -124,7 +124,7 @@ </conditional> <conditional name="set_cosmic"> - <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio"> + <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> @@ -136,8 +136,11 @@ <option value="v2" selected="true">Cosmic v2, March 2015</option> <option value="v3">Cosmic v3, May 2019</option> </param> - <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?" - help="Output the normalized signatures contributions for further visualization" /> + <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" + help="Output the normalized signatures contributions for further visualization" > + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> </when> <when value="no" /> </conditional> @@ -157,7 +160,7 @@ <filter>set_cosmic['choices'] == "yes"</filter> </data> <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table"> - <filter>set_cosmic['contrib_matrix_out']</filter> + <filter>set_cosmic['choices'] == "yes" and set_cosmic['contrib_matrix_out'] == "yes"</filter> </data> <data name="rdata" format="rdata" label="${tool.name}: RData file"> @@ -166,6 +169,82 @@ </outputs> <tests> + <!-- cosmic signatures with cosmic V3 --> + <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="yes" /> + <param name="cosmic_version" value="v3"/> + </conditional> + <param name="signum" value="3" /> + <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/> + <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/> + </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="yes" /> + </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> + <!-- simple profile --> <test> <param name="vcfs"> @@ -219,53 +298,6 @@ <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>