Mercurial > repos > iuc > limma_voom

diff limma_voom.R @ 13:d5a940112511 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
author iuc
date Sun, 30 Sep 2018 10:51:29 -0400
parents 81796eb60bd0
children 3133e833b3ce
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line diff
--- a/limma_voom.R	Sun Aug 05 05:13:12 2018 -0400
+++ b/limma_voom.R	Sun Sep 30 10:51:29 2018 -0400
@@ -371,8 +371,8 @@
     topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv"))
     glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html"))
 }
-filtOut <- makeOut(paste0(deMethod, "_filtcounts.tsv"))
-normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
+filtOut <- makeOut(paste0(deMethod, "_", "filtcounts"))
+normOut <- makeOut(paste0(deMethod, "_", "normcounts"))
 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
 sessionOut <- makeOut("session_info.txt")
 
@@ -451,7 +451,7 @@
         print("Outputting filtered counts")
         filt_counts <- data.frame(data$genes, data$counts)
         write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE)
-        linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts.tsv"), stringsAsFactors=FALSE))
+        linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts"), stringsAsFactors=FALSE))
     }
 
     # Plot Density
@@ -723,7 +723,7 @@
     # Save normalised counts (log2cpm)
     if (wantNorm) {
         write.table(logCPM, file=normOut, row.names=TRUE, sep="\t", quote=FALSE)
-        linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
+        linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts"))))
     }
 } else {
     # limma-voom approach
@@ -774,7 +774,7 @@
     if (wantNorm) {
         norm_counts <- data.frame(vData$genes, vData$E)
         write.table(norm_counts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE)
-        linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
+        linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts"))))
     }
 
     # Fit linear model and estimate dispersion with eBayes
@@ -1052,7 +1052,9 @@
 
 cata("<h4>Tables:</h4>\n")
 for (i in 1:nrow(linkData)) {
-    if (grepl(".tsv", linkData$Link[i])) {
+    if (grepl("counts$", linkData$Link[i])) {
+        HtmlLink(linkData$Link[i], linkData$Label[i])
+    } else if (grepl(".tsv", linkData$Link[i])) {
         HtmlLink(linkData$Link[i], linkData$Label[i])
     }
 }