diff mutational_patterns.xml @ 14:56c8869a231e draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 518fb067e8206ecafbf673a5e4cf375ccead11e3"

--- a/mutational_patterns.xml	Thu Oct 22 23:29:28 2020 +0000
+++ b/mutational_patterns.xml	Fri Jun 04 22:35:48 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy13.1">
+<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>
@@ -6,19 +6,23 @@
         <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="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
-        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
+<!--
         <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
-        <!-- install bioconda genomes
-        bioconductor-bsgenome.mmusculus.ucsc.mm9
-        bioconductor-bsgenome.mmusculus.ucsc.mm10   -->                    
+        <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[ 
+    <command detect_errors="exit_code"><![CDATA[
 #import json
 #import os
 Rscript $__tool_directory__/mutational_patterns.R 
@@ -63,8 +67,8 @@
     <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.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>
@@ -280,7 +284,7 @@
 * 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 in their mutational pattern
+* 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