Mercurial > repos > galaxyp > dialignr

comparison dialignr.R @ 0:fbbbf8c145fc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
author galaxyp
date Wed, 30 Dec 2020 20:12:57 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:fbbbf8c145fc
1 library(DIAlignR)
2
3 ## Parse command line arguments
4 args <- commandArgs(trailingOnly = TRUE)
5
6 hh <- paste(unlist(args), collapse = " ")
7 listoptions <- unlist(strsplit(hh, "--"))[-1]
8 options.args <- sapply(listoptions, function(x) {
9 unlist(strsplit(x, " "))[-1]
10 })
11 options.names <- sapply(listoptions, function(x) {
12 option <- unlist(strsplit(x, " "))[1]
13 })
14 names(options.args) <- unlist(options.names)
15 ##
16
17 data_path <- "./data/"
18 runs_file_path <- "./runs.txt"
19
20 runs <- readLines(runs_file_path)
21
22 alignTargetedRuns(dataPath = data_path,
23 outFile = "alignedTargetedRuns.csv",
24 runs = runs,
25 oswMerged = as.logical(options.args["oswMerged"]),
26 maxFdrQuery = as.numeric(options.args["maxFdrQuery"]),
27 XICfilter = options.args["XICfilter"],
28 polyOrd = as.integer(options.args["polyOrd"]),
29 kernelLen = as.integer(options.args["kernelLen"]),
30 globalAlignment = options.args["globalAlignment"],
31 globalAlignmentFdr = as.numeric(options.args["globalAlignmentFdr"]),
32 globalAlignmentSpan = as.numeric(options.args["globalAlignmentSpan"]),
33 RSEdistFactor = as.numeric(options.args["RSEdistFactor"]),
34 normalization = options.args["normalization"],
35 simMeasure = options.args["simMeasure"],
36 alignType = options.args["alignType"],
37 goFactor = as.numeric(options.args["goFactor"]),
38 geFactor = as.numeric(options.args["geFactor"]),
39 cosAngleThresh = as.numeric(options.args["cosAngleThresh"]),
40 OverlapAlignment = as.logical(options.args["OverlapAlignment"]),
41 dotProdThresh = as.numeric(options.args["dotProdThresh"]),
42 gapQuantile = as.numeric(options.args["gapQuantile"]),
43 hardConstrain = as.logical(options.args["hardConstrain"]),
44 samples4gradient = as.numeric(options.args["samples4gradient"]),
45 analyteFDR = as.numeric(options.args["analyteFDR"]),
46 unalignedFDR = as.numeric(options.args["unalignedFDR"]),
47 alignedFDR = as.numeric(options.args["alignedFDR"]),
48 baselineType = options.args["baselineType"],
49 integrationType = options.args["integrationType"],
50 fitEMG = as.logical(options.args["fitEMG"]),
51 recalIntensity = as.logical(options.args["recalIntensity"]),
52 fillMissing = as.logical(options.args["fillMissing"]),
53 smoothPeakArea = as.logical(options.args["smoothPeakArea"])
54 )