Mercurial > repos > tomnl > anticipated_purity_lcms
annotate assess_purity_msms.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 | b83bcc259b76 |
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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:
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1 library(msPurity) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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2 library(optparse) |
2
b83bcc259b76
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
0
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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:
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4 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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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
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6 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
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7 make_option("--mzML_files", type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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8 make_option("--galaxy_names", type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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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:
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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:
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12 make_option("--iwNorm", default="none", type="character"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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13 make_option("--exclude_isotopes", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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14 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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15 make_option("--mostIntense", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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16 make_option("--plotP", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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17 make_option("--nearest", action="store_true"), |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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18 make_option("--cores", default=4) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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19 ) |
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 # store options |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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22 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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23 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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24 minOffset = as.numeric(opt$minOffset) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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25 maxOffset = as.numeric(opt$maxOffset) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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26 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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27 if (opt$iwNorm=='none'){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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28 iwNorm = FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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29 iwNormFun = NULL |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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30 }else if (opt$iwNorm=='gauss'){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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31 iwNorm = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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32 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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33 }else if (opt$iwNorm=='rcosine'){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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34 iwNorm = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
changeset
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35 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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36 }else if (opt$iwNorm=='QE5'){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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37 iwNorm = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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38 iwNormFun = msPurity::iwNormQE.5() |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff
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39 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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40 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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41 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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42 filepaths <- filepaths[filepaths != ""] |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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43 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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44 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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45 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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46 if(is.null(opt$minOffset) || is.null(opt$maxOffset)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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47 offsets = NA |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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48 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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49 offsets = as.numeric(c(opt$minOffset, opt$maxOffset)) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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50 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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51 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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52 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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53 if(is.null(opt$mostIntense)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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54 mostIntense = FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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55 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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56 mostIntense = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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57 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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58 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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59 if(is.null(opt$nearest)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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60 nearest = FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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61 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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62 nearest = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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63 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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64 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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65 if(is.null(opt$plotP)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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66 plotP = FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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67 plotdir = NULL |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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68 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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69 plotP = TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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70 plotdir = opt$out_dir |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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71 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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72 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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73 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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74 if (is.null(opt$isotope_matrix)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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75 im <- NULL |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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76 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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77 im <- read.table(opt$isotope_matrix, |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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78 header = TRUE, sep='\t', stringsAsFactors = FALSE) |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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79 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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80 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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81 if (is.null(opt$exclude_isotopes)){ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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82 isotopes <- FALSE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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83 }else{ |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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84 isotopes <- TRUE |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
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85 } |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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parents:
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86 |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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87 pa <- msPurity::purityA(filepaths, |
dc00b7222a3c
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
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88 cores = opt$cores, |
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89 mostIntense = mostIntense, |
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90 nearest = nearest, |
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91 offsets = offsets, |
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92 plotP = plotP, |
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93 plotdir = plotdir, |
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94 interpol = "linear", |
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95 iwNorm = iwNorm, |
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96 iwNormFun = iwNormFun, |
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97 ilim = opt$ilim, |
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98 mzRback = "pwiz", |
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99 isotopes = isotopes, |
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100 im = im) |
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101 |
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102 |
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103 if (!is.null(opt$galaxy_names)){ |
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104 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) |
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105 galaxy_names <- galaxy_names[galaxy_names != ""] |
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106 names(pa@fileList) <- galaxy_names |
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107 } |
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108 |
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109 print(pa) |
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110 |
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111 save(pa, file=file.path(opt$out_dir, 'purity_msms.RData')) |
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112 |
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113 print(head(pa@puritydf)) |
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114 write.table(pa@puritydf, file.path(opt$out_dir, 'purity_msms.tsv'), row.names=FALSE, sep='\t') |
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115 |
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116 # removed_peaks <- data.frame(removed_peaks) |
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117 # write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), |
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118 # file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t') |