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