# HG changeset patch
# User iuc
# Date 1528438816 14400
# Node ID e26047c4562dcaf1753c7ed5589bbaa4f06cabba
# Parent  4255881bebb199b715e3d7170ab0fa3bfaebcd46
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3

diff -r 4255881bebb1 -r e26047c4562d limma_voom.R
--- a/limma_voom.R	Tue Jun 05 04:28:56 2018 -0400
+++ b/limma_voom.R	Fri Jun 08 02:20:16 2018 -0400
@@ -808,9 +808,12 @@
     linkData <- rbind(linkData, c(linkName, linkAddr))
     invisible(dev.off())
 
-    # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene names in 2nd column)
+    # Generate Glimma interactive MD plot and table, requires annotation file (assumes gene labels/symbols in 2nd column)
     if (haveAnno) {
-        Glimma::glMDPlot(fit, coef=i, counts=y$counts, anno=y$genes, groups=factors[, 1],
+        # make gene labels unique to handle NAs
+        geneanno <- y$genes
+        geneanno[, 2] <- make.unique(geneanno[, 2])
+        Glimma::glMDPlot(fit, coef=i, counts=y$counts, 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)
diff -r 4255881bebb1 -r e26047c4562d limma_voom.xml
--- a/limma_voom.xml	Tue Jun 05 04:28:56 2018 -0400
+++ b/limma_voom.xml	Fri Jun 08 02:20:16 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.34.9.5">
+<tool id="limma_voom" name="limma" version="3.34.9.6">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -210,7 +210,7 @@
 
         <!-- Contrasts -->
         <repeat name="rep_contrast" title="Contrast" min="1" default="1">
-            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
+            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
                 <validator type="empty_field" />
                 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
             </param>