Merge pull request #6 from biowdl/mergeCounts

add merge counts

mergecounts.wdl

+task MergeCounts {
+    String? preCommand
+
+    Array[File] inputFiles
+    String outputFile
+    String idVar
+    String measurementVar
+
+    # Based on a script by Szymon Kielbasa/Ioannis Moustakas
+    command <<<
+        set -e -o pipefail
+        ${preCommand}
+        R --no-save --slave <<CODE > ${outputFile}
+            library(dplyr)
+            library(reshape2)
+
+            listOfFiles <- c("${sep='", "' inputFiles}")
+
+            d <- do.call(rbind, lapply(listOfFiles, function(file){
+                d <- read.table(file, header=TRUE, comment.char="#")
+                colI <- grep(${measurementVar}, colnames(d))
+                colnames(d)[colI] <- strsplit(file, "/")[[1]][3]
+                d <- d %>% melt(id.vars=${idVar}, measure.vars=colI,
+                    variable.name="sample", value.name="count")
+            }))
+
+            d <- d %>% dcast(paste0(${idVar}, " ~ sample"), value.var="count")
+            write.table(d, sep="\t", quote=FALSE, row.names=FALSE)
+        CODE
+    >>>
+
+    output {
+        File mergedCounts = outputFile
+    }
+}
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