Mercurial > repos > artbio > mutational_patterns
diff mutational_patterns.xml @ 17:8c6ee1c2248f draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"
| author | artbio |
|---|---|
| date | Tue, 05 Oct 2021 22:28:34 +0000 |
| parents | 31e7a33ecd71 |
| children | 8d9f31389f33 |
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--- a/mutational_patterns.xml Mon Oct 04 00:35:06 2021 +0000 +++ b/mutational_patterns.xml Tue Oct 05 22:28:34 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy1"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy2"> <description>from genomic variations in vcf files</description> <requirements> <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> @@ -25,7 +25,7 @@ <command detect_errors="exit_code"><![CDATA[ #import json #import os -Rscript $__tool_directory__/mutational_patterns.R +Rscript $__tool_directory__/mutational_patterns.R --inputs #set $filename_to_element_identifiers = {} #for $sample in $vcfs: @@ -62,6 +62,8 @@ #if $rdata_out --rdata '$rdata' #end if + + --tooldir '$__tool_directory__/' ]]></command> <inputs> @@ -135,6 +137,8 @@ <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> + <option value="v3.1">Cosmic v3.1, June 2020</option> + <option value="v3.2">Cosmic v3.2, March 2021</option> </param> <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" help="Output the normalized signatures contributions for further visualization" >