diff mutational_patterns.xml @ 17:8c6ee1c2248f draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e5d498dfc5a6a9aaea3d09037dea5d15c2d85dd2"

--- 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" >