Mercurial > repos > tomnl > anticipated_purity_lcms
annotate anticipated_purity_dims.R @ 22:c8b34df46dae draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author | tomnl |
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date | Fri, 01 Jun 2018 13:41:15 -0400 |
parents | e05068fe15a1 |
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rev | line source |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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1 library(msPurity) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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2 library(optparse) |
2
b83bcc259b76
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
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3 print(sessionInfo()) |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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4 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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5 option_list <- list( |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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6 make_option(c("--mzML_file"), type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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7 make_option(c("--peaks_file"), type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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8 make_option(c("-o", "--out_dir"), type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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9 make_option("--minOffset", default=0.5), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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10 make_option("--maxOffset", default=0.5), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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11 make_option("--ilim", default=0.05), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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12 make_option("--ppm", default=4), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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13 make_option("--dimspy", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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14 make_option("--sim", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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15 make_option("--remove_nas", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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16 make_option("--iwNorm", default="none", type="character"), |
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079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
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17 make_option("--file_num_dimspy", default=1), |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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18 make_option("--exclude_isotopes", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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19 make_option("--isotope_matrix", type="character") |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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20 ) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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21 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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22 # store options |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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23 opt<- parse_args(OptionParser(option_list=option_list)) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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24 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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25 print(sessionInfo()) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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26 print(opt) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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27 |
6
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
2
diff
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28 if (is.null(opt$dimspy)){ |
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
2
diff
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29 |
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
2
diff
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30 df <- read.table(opt$peaks_file, header = TRUE, sep='\t') |
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
2
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31 filename = NA |
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e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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32 mzml_file <- opt$mzML_file |
6
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents:
2
diff
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33 }else{ |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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34 indf <- read.table(opt$peaks_file, |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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35 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
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e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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36 |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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37 |
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e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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38 if (file.exists(opt$mzML_file)){ |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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39 mzml_file <- opt$mzML_file |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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40 }else{ |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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41 |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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42 filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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43 print(filename) |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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44 # check if the data file is mzML or RAW (can only use mzML currently) so |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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45 # we expect an mzML file of the same name in the same folder |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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46 indf$i <- indf[,colnames(indf)==filename] |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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47 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
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48 |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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49 filename = sub("raw", "mzML", filename, ignore.case = TRUE) |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
diff
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50 print(filename) |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
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51 |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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52 mzml_file <- file.path(opt$mzML_file, filename) |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
11
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53 |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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54 } |
e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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55 |
11
2ccfae7470b3
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
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56 df <- indf[4:nrow(indf),] |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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57 if ('blank_flag' %in% colnames(df)){ |
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e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents:
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58 df <- df[df$blank_flag==1,] |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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59 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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60 colnames(df)[colnames(df)=='m.z'] <- 'mz' |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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61 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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62 if ('nan' %in% df$mz){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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63 df[df$mz=='nan',]$mz <- NA |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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64 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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65 df$mz <- as.numeric(df$mz) |
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e05068fe15a1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
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66 |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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67 |
6
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
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68 |
079bdef733e8
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
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69 |
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dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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70 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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71 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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72 if (!is.null(opt$remove_nas)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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73 df <- df[!is.na(df$mz),] |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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74 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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75 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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76 if (is.null(opt$isotope_matrix)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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77 im <- NULL |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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78 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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79 im <- read.table(opt$isotope_matrix, |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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80 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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81 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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82 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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83 if (is.null(opt$exclude_isotopes)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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84 isotopes <- FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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85 }else{ |
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86 isotopes <- TRUE |
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87 } |
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88 |
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89 |
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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90 |
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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91 if (is.null(opt$sim)){ |
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92 sim=FALSE |
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93 }else{ |
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94 sim=TRUE |
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95 } |
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96 |
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97 minOffset = as.numeric(opt$minOffset) |
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98 maxOffset = as.numeric(opt$maxOffset) |
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99 |
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100 |
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101 |
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102 if (opt$iwNorm=='none'){ |
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103 iwNorm = FALSE |
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104 iwNormFun = NULL |
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105 }else if (opt$iwNorm=='gauss'){ |
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106 iwNorm = TRUE |
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107 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) |
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108 }else if (opt$iwNorm=='rcosine'){ |
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109 iwNorm = TRUE |
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110 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) |
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111 }else if (opt$iwNorm=='QE5'){ |
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112 iwNorm = TRUE |
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113 iwNormFun = msPurity::iwNormQE.5() |
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114 } |
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115 |
7
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116 print('FIRST ROWS OF PEAK FILE') |
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117 print(head(df)) |
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118 print(mzml_file) |
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119 predicted <- msPurity::dimsPredictPuritySingle(df$mz, |
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120 filepth=mzml_file, |
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121 minOffset=minOffset, |
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122 maxOffset=maxOffset, |
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123 ppm=opt$ppm, |
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124 mzML=TRUE, |
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125 sim = sim, |
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126 ilim = opt$ilim, |
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127 isotopes = isotopes, |
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128 im = im, |
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129 iwNorm = iwNorm, |
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130 iwNormFun = iwNormFun |
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131 ) |
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132 predicted <- cbind(df, predicted) |
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133 |
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134 print(head(predicted)) |
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135 print(file.path(opt$out_dir, 'anticipated_purity_dims.tsv')) |
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136 write.table(predicted, file.path(opt$out_dir, 'anticipated_purity_dims.tsv'), row.names=FALSE, sep='\t') |