Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra
annotate purityA.R @ 7:2e10c13085c9 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
author | computational-metabolomics |
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date | Tue, 08 Feb 2022 14:02:03 +0000 |
parents | cc0f8ddad4a8 |
children | a46824d13914 |
rev | line source |
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0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff
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1 library(msPurity) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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2 library(optparse) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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3 print(sessionInfo()) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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5 option_list <- list( |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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6 make_option(c("-o", "--out_dir"), type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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7 make_option("--mzML_files", type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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8 make_option("--galaxy_names", type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
diff
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9 make_option("--minOffset", type = "numeric"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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10 make_option("--maxOffset", type = "numeric"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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11 make_option("--ilim", type = "numeric"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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12 make_option("--iwNorm", default = "none", type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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13 make_option("--exclude_isotopes", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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14 make_option("--isotope_matrix", type = "character"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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15 make_option("--mostIntense", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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16 make_option("--plotP", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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17 make_option("--nearest", action = "store_true"), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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18 make_option("--cores", default = 4), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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19 make_option("--ppmInterp", default = 7) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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20 ) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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21 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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22 opt <- parse_args(OptionParser(option_list = option_list)) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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23 print(opt) |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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24 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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25 if (opt$iwNorm == "none") { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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26 iwNorm <- FALSE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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27 iwNormFun <- NULL |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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28 }else if (opt$iwNorm == "gauss") { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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29 iwNorm <- TRUE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
diff
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30 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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31 print("User has to define offsets if using Gaussian normalisation") |
1
1e6b7c4d99cd
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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32 }else{ |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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33 iwNormFun <- msPurity::iwNormGauss(minOff = -as.numeric(opt$minOffset), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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34 maxOff = as.numeric(opt$maxOffset)) |
1
1e6b7c4d99cd
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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35 } |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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36 }else if (opt$iwNorm == "rcosine") { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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37 iwNorm <- TRUE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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38 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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39 print("User has to define offsets if using R-cosine normalisation") |
1
1e6b7c4d99cd
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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0
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40 }else{ |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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1
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41 iwNormFun <- msPurity::iwNormRcosine(minOff = -as.numeric(opt$minOffset), |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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42 maxOff = as.numeric(opt$maxOffset)) |
1
1e6b7c4d99cd
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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43 } |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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44 }else if (opt$iwNorm == "QE5") { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
1
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45 iwNorm <- TRUE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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46 iwNormFun <- msPurity::iwNormQE.5() |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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48 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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49 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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50 filepaths <- filepaths[filepaths != ""] |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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52 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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53 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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54 if (is.null(opt$minOffset) || is.null(opt$maxOffset)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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55 offsets <- NA |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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56 }else{ |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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57 offsets <- as.numeric(c(opt$minOffset, opt$maxOffset)) |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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58 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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59 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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60 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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61 if (is.null(opt$mostIntense)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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62 mostIntense <- FALSE |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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63 }else{ |
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cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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64 mostIntense <- TRUE |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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65 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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66 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67 if (is.null(opt$nearest)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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68 nearest <- FALSE |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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69 }else{ |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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70 nearest <- TRUE |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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71 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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72 |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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73 if (is.null(opt$plotP)) { |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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74 plotP <- FALSE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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75 plotdir <- NULL |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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76 }else{ |
6
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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77 plotP <- TRUE |
cc0f8ddad4a8
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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78 plotdir <- opt$out_dir |
0
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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79 } |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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80 |
96af79da0cc6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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81 |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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82 if (is.null(opt$isotope_matrix)) { |
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83 im <- NULL |
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84 }else{ |
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85 im <- read.table(opt$isotope_matrix, |
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86 header = TRUE, sep = "\t", stringsAsFactors = FALSE) |
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87 } |
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88 |
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89 if (is.null(opt$exclude_isotopes)) { |
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90 isotopes <- FALSE |
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91 }else{ |
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92 isotopes <- TRUE |
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93 } |
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94 |
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95 pa <- msPurity::purityA(filepaths, |
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96 cores = opt$cores, |
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97 mostIntense = mostIntense, |
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98 nearest = nearest, |
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99 offsets = offsets, |
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100 plotP = plotP, |
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101 plotdir = plotdir, |
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102 interpol = "linear", |
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103 iwNorm = iwNorm, |
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104 iwNormFun = iwNormFun, |
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105 ilim = opt$ilim, |
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106 mzRback = "pwiz", |
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107 isotopes = isotopes, |
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108 im = im, |
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109 ppmInterp = opt$ppmInterp) |
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110 |
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111 |
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112 if (!is.null(opt$galaxy_names)) { |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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113 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]]) |
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114 galaxy_names <- galaxy_names[galaxy_names != ""] |
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115 names(pa@fileList) <- galaxy_names |
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116 } |
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117 |
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118 print(pa) |
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119 save(pa, file = file.path(opt$out_dir, "purityA_output.RData")) |
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120 |
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121 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)]) |
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122 |
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123 print(head(pa@puritydf)) |
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124 write.table(pa@puritydf, file.path(opt$out_dir, "purityA_output.tsv"), row.names = FALSE, sep = "\t") |