Add templates for plotting scripts and their wrappers

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/plot_heatmap.R

+#!/usr/bin/env Rscript
+#
+# Script for plotting heatmap for the Gentrap pipeline
+
+
+# General function to install package if it does not exist
+# Otherwise, it only loads the package
+usePackage <- function(p) {
+    r <- getOption("repos")
+    r["CRAN"] <- "http://cran.us.r-project.org"
+    options(repos = r)
+    rm(r)
+    if (!is.element(p, installed.packages()[,1]))
+        install.packages(p, dep = TRUE)
+    require(p, character.only = TRUE)
+}
+
+usePackage("getopt")
+usePackage("edgeR")
+usePackage("ggplot2")
+usePackage("gplots")
+usePackage("grid")
+usePackage("jsonlite")
+usePackage("reshape2")
+usePackage("MASS")
+usePackage("RColorBrewer")
+
+# create spec for arg parsing
+spec <- matrix(c(
+      # input table (merge of all samples)
+      'input-table',   'I', 1, 'character',
+      # output plot file
+      'output-plot',   'O', 1, 'character',
+      # perform TMM-normalization (only if we are dealing with count data)
+      'tmm-normalize', 'T', 0, 'logical'
+      # help
+      'help',          'H', 0, 'logical'
+), byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+# print help if requested
+if (!is.null(opt[['help']])) {
+  cat(getopt(spec, usage=TRUE))
+  q(status=1)
+}

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/plot_pca.R

+#!/usr/bin/env Rscript
+#
+# Script for plotting PCA plots for the Gentrap pipeline
+
+
+# General function to install package if it does not exist
+# Otherwise, it only loads the package
+usePackage <- function(p) {
+    r <- getOption("repos")
+    r["CRAN"] <- "http://cran.us.r-project.org"
+    options(repos = r)
+    rm(r)
+    if (!is.element(p, installed.packages()[,1]))
+        install.packages(p, dep = TRUE)
+    require(p, character.only = TRUE)
+}
+
+usePackage("getopt")
+usePackage("edgeR")
+usePackage("ggplot2")
+usePackage("gplots")
+usePackage("grid")
+usePackage("jsonlite")
+usePackage("reshape2")
+usePackage("MASS")
+usePackage("RColorBrewer")
+
+# create spec for arg parsing
+spec <- matrix(c(
+      # input table (merge of all samples)
+      'input-table',   'I', 1, 'character',
+      # output plot file
+      'output-plot',   'O', 1, 'character',
+      # perform TMM-normalization (only if we are dealing with count data)
+      'tmm-normalize', 'T', 0, 'logical'
+      # help
+      'help',          'H', 0, 'logical'
+), byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+# print help if requested
+if (!is.null(opt[['help']])) {
+  cat(getopt(spec, usage=TRUE))
+  q(status=1)
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala

+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author  Wibowo Arindrarto
+ */
+
+package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Wrapper for the plot_heatmap.R script, used internally in Gentrap
+ */
+class PlotHeatmap(val root: Configurable) extends RScriptCommandLineFunction {
+
+  setRScript("plot_heatmap.R", "/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/")
+
+  @Input(doc = "Input table", required = true)
+  var input: File = null
+
+  @Output(doc = "Output plot", required = false)
+  var output: File = null
+
+  var tmmNormalize: Boolean = config("tmm_normalize", default = false)
+
+  def cmdLine = {
+    RScriptCommand +
+      conditional(tmmNormalize, "-T") +
+      required("-I", input) +
+      required("-O", output)
+  }
+}

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala

+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author  Wibowo Arindrarto
+ */
+
+package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Wrapper for the plot_pca.R script, used internally in Gentrap
+ */
+class PlotPca(val root: Configurable) extends RScriptCommandLineFunction {
+
+  setRScript("plot_pca.R", "/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/")
+
+  @Input(doc = "Input table", required = true)
+  var input: File = null
+
+  @Output(doc = "Output plot", required = false)
+  var output: File = null
+
+  var tmmNormalize: Boolean = config("tmm_normalize", default = false)
+
+  def cmdLine = {
+    RScriptCommand +
+      conditional(tmmNormalize, "-T") +
+      required("-I", input) +
+      required("-O", output)
+  }
+}