# HG changeset patch
# User artbio
# Date 1603119354 0
# Node ID 4ff3c984523bc855cff0c843a5b1264a5ca6a110
# Parent  e0dad46148bfef0bcf44834a83fd9e3bae93581a
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 109570d3d5f2c232d3bc976590295c1b83bfc9c3"

diff -r e0dad46148bf -r 4ff3c984523b mutational_patterns.R
--- a/mutational_patterns.R	Mon Oct 19 07:47:24 2020 +0000
+++ b/mutational_patterns.R	Mon Oct 19 14:55:54 2020 +0000
@@ -316,10 +316,11 @@
              worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))]
         }
         worklist <- as.data.frame(melt(worklist))
+        worklist[,2] <- paste0(worklist[,2], " - ", worklist[,4])
+        head(worklist)
     }
     
     colnames(worklist) <- c("signature", "sample", "value", "level")
-    print(worklist)
     worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100))
     worklist$pos <- cumsum(worklist$value) - worklist$value/2
     worklist$label <- factor(worklist$signature)
diff -r e0dad46148bf -r 4ff3c984523b mutational_patterns.xml
--- a/mutational_patterns.xml	Mon Oct 19 07:47:24 2020 +0000
+++ b/mutational_patterns.xml	Mon Oct 19 14:55:54 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy9">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy10">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
diff -r e0dad46148bf -r 4ff3c984523b test-data/cosmic_output1.pdf
Binary file test-data/cosmic_output1.pdf has changed
diff -r e0dad46148bf -r 4ff3c984523b test-data/cosmic_output2.pdf
Binary file test-data/cosmic_output2.pdf has changed