diff dialignr.R @ 0:fbbbf8c145fc draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dialignr.R	Wed Dec 30 20:12:57 2020 +0000
@@ -0,0 +1,54 @@
+library(DIAlignR)
+
+## Parse command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+hh <- paste(unlist(args), collapse = " ")
+listoptions <- unlist(strsplit(hh, "--"))[-1]
+options.args <- sapply(listoptions, function(x) {
+                  unlist(strsplit(x, " "))[-1]
+                })
+options.names <- sapply(listoptions, function(x) {
+                  option <- unlist(strsplit(x, " "))[1]
+                })
+names(options.args) <- unlist(options.names)
+##
+
+data_path <- "./data/"
+runs_file_path <- "./runs.txt"
+
+runs <- readLines(runs_file_path)
+
+alignTargetedRuns(dataPath = data_path,
+                  outFile = "alignedTargetedRuns.csv",
+                  runs = runs,
+                  oswMerged = as.logical(options.args["oswMerged"]),
+                  maxFdrQuery = as.numeric(options.args["maxFdrQuery"]),
+                  XICfilter = options.args["XICfilter"],
+                  polyOrd = as.integer(options.args["polyOrd"]),
+                  kernelLen = as.integer(options.args["kernelLen"]),
+                  globalAlignment = options.args["globalAlignment"],
+                  globalAlignmentFdr = as.numeric(options.args["globalAlignmentFdr"]),
+                  globalAlignmentSpan = as.numeric(options.args["globalAlignmentSpan"]),
+                  RSEdistFactor = as.numeric(options.args["RSEdistFactor"]),
+                  normalization = options.args["normalization"],
+                  simMeasure = options.args["simMeasure"],
+                  alignType = options.args["alignType"],
+                  goFactor = as.numeric(options.args["goFactor"]),
+                  geFactor = as.numeric(options.args["geFactor"]),
+                  cosAngleThresh = as.numeric(options.args["cosAngleThresh"]),
+                  OverlapAlignment = as.logical(options.args["OverlapAlignment"]),
+                  dotProdThresh = as.numeric(options.args["dotProdThresh"]),
+                  gapQuantile = as.numeric(options.args["gapQuantile"]),
+                  hardConstrain = as.logical(options.args["hardConstrain"]),
+                  samples4gradient = as.numeric(options.args["samples4gradient"]),
+                  analyteFDR = as.numeric(options.args["analyteFDR"]),
+                  unalignedFDR = as.numeric(options.args["unalignedFDR"]),
+                  alignedFDR = as.numeric(options.args["alignedFDR"]),
+                  baselineType = options.args["baselineType"],
+                  integrationType = options.args["integrationType"],
+                  fitEMG = as.logical(options.args["fitEMG"]),
+                  recalIntensity = as.logical(options.args["recalIntensity"]),
+                  fillMissing = as.logical(options.args["fillMissing"]),
+                  smoothPeakArea = as.logical(options.args["smoothPeakArea"])
+)