# HG changeset patch
# User artbio
# Date 1603150498 0
# Node ID 59c0e2a7965c0a8513a222977c4c76e29f0089b9
# Parent  4ff3c984523bc855cff0c843a5b1264a5ca6a110
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 533394bd219d56cde7fb9721803e8aed8fd5a25d"

diff -r 4ff3c984523b -r 59c0e2a7965c mutational_patterns.R
--- a/mutational_patterns.R	Mon Oct 19 14:55:54 2020 +0000
+++ b/mutational_patterns.R	Mon Oct 19 23:34:58 2020 +0000
@@ -316,7 +316,7 @@
              worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))]
         }
         worklist <- as.data.frame(melt(worklist))
-        worklist[,2] <- paste0(worklist[,2], " - ", worklist[,4])
+        worklist[,2] <- paste0(worklist[,4], " - ", worklist[,2])
         head(worklist)
     }
     
@@ -328,7 +328,7 @@
     p7 <-  ggplot(worklist, aes(x="", y=value, group=signature, fill=signature)) +
               geom_bar(width = 1, stat = "identity") +
               geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) +
-              coord_polar("y", start=0) + facet_wrap(~ sample) +
+              coord_polar("y", start=0) + facet_wrap(.~sample) +
               labs(x="", y="Samples", fill = cosmic_tag) +
               scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
                                 values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) +
diff -r 4ff3c984523b -r 59c0e2a7965c mutational_patterns.xml
--- a/mutational_patterns.xml	Mon Oct 19 14:55:54 2020 +0000
+++ b/mutational_patterns.xml	Mon Oct 19 23:34:58 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy10">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy11">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
diff -r 4ff3c984523b -r 59c0e2a7965c test-data/cosmic_output1.pdf
Binary file test-data/cosmic_output1.pdf has changed