# HG changeset patch
# User iuc
# Date 1557061324 14400
# Node ID 97e06a4c7c75e2b28b92f4358c5a9d1bf62c21e4
# Parent  86b3df7db58b1f24ad6a803aa1c48af6aabc05f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666

diff -r 86b3df7db58b -r 97e06a4c7c75 limma_voom.R
--- a/limma_voom.R	Mon Feb 18 17:49:24 2019 -0500
+++ b/limma_voom.R	Sun May 05 09:02:04 2019 -0400
@@ -879,8 +879,15 @@
         geneanno <- y$genes
         geneanno[, 2] <- make.unique(geneanno[, 2])
 
+        # use the logCPMS for the counts
+        if (wantTrend) {
+            cnts <- logCPM
+        } else{
+            cnts <- vData$E
+        }
+
         # MD plot
-        Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=geneanno, groups=factors[, 1],
+        Glimma::glMDPlot(fit, coef=i, counts=cnts, anno=geneanno, groups=factors[, 1],
              status=status[, i], sample.cols=col.group,
              main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2],
              folder=paste0("glimma_", unmake.names(con)), launch=FALSE)
@@ -889,10 +896,10 @@
         linkData <- rbind(linkData, c(linkName, linkAddr))
 
         # Volcano plot
-        Glimma::glXYPlot(x=fit$coefficients[, i], y=fit$lods[, i], counts=y$counts, anno=geneanno, groups=factors[, 1], 
+        Glimma::glXYPlot(x=fit$coefficients[, i], y=-log10(fit$p.value[, i]), counts=cnts, anno=geneanno, groups=factors[, 1],
             status=status[, i], sample.cols=col.group,
             main=paste("Volcano Plot:", unmake.names(con)), side.main=colnames(y$genes)[2],
-            xlab="logFC", ylab="logodds",
+            xlab="logFC", ylab="-log10(P-value)",
             folder=paste0("glimma_volcano_", unmake.names(con)), launch=FALSE)
         linkName <- paste0("Glimma_VolcanoPlot_", con, ".html")
         linkAddr <- paste0("glimma_volcano_", con, "/XY-Plot.html")
diff -r 86b3df7db58b -r 97e06a4c7c75 limma_voom.xml
--- a/limma_voom.xml	Mon Feb 18 17:49:24 2019 -0500
+++ b/limma_voom.xml	Sun May 05 09:02:04 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.38.3+galaxy1">
+<tool id="limma_voom" name="limma" version="3.38.3+galaxy2">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>