Mercurial > repos > computational-metabolomics > mspurity_createdatabase
annotate frag4feature.R @ 4:3d36a391612c draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
author | computational-metabolomics |
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date | Mon, 10 Aug 2020 08:41:22 -0400 |
parents | f52287a06c02 |
children | 2f71b3495221 |
rev | line source |
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0
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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1 library(optparse) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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2 library(msPurity) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 library(xcms) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4 print(sessionInfo()) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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5 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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6 xset_pa_filename_fix <- function(opt, pa, xset=NULL){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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7 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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8 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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11 # needs to be done due to Galaxy moving the files around and screwing up any links to files |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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12 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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13 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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14 filepaths <- filepaths[filepaths != ""] |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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15 new_names <- basename(filepaths) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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16 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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18 galaxy_names <- galaxy_names[galaxy_names != ""] |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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19 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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20 nsave <- names(pa@fileList) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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21 old_filenames <- basename(pa@fileList) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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22 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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24 names(pa@fileList) <- nsave |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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25 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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28 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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29 print(pa@fileList) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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30 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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31 if(!is.null(xset)){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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32 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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33 print(xset@filepaths) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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34 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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35 if(!all(basename(pa@fileList)==basename(xset@filepaths))){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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36 if(!all(names(pa@fileList)==basename(xset@filepaths))){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 print('FILELISTS DO NOT MATCH') |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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38 message('FILELISTS DO NOT MATCH') |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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39 quit(status = 1) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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40 }else{ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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41 xset@filepaths <- unname(pa@fileList) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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42 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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43 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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44 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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45 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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46 return(list(pa, xset)) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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48 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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49 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50 option_list <- list( |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 make_option(c("-o", "--out_dir"), type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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52 make_option("--pa", type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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53 make_option("--xset", type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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54 make_option("--ppm", default=10), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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55 make_option("--plim", default=0.0), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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56 make_option("--convert2RawRT", action="store_true"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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57 make_option("--intense", action="store_true"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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58 make_option("--createDB", action="store_true"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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59 make_option("--cores", default=4), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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60 make_option("--mzML_files", type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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61 make_option("--galaxy_names", type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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62 make_option("--grp_peaklist", type="character"), |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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63 make_option("--useGroup", action="store_true") |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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64 ) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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65 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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66 # store options |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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67 opt<- parse_args(OptionParser(option_list=option_list)) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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68 print(opt) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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69 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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70 loadRData <- function(rdata_path, name){ |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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71 #loads an RData file, and returns the named xset object if it is there |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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72 load(rdata_path) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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73 return(get(ls()[ls() %in% name])) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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74 } |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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75 |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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76 # This function retrieve a xset like object |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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78 getxcmsSetObject <- function(xobject) { |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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79 # XCMS 1.x |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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80 if (class(xobject) == "xcmsSet") |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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81 return (xobject) |
f52287a06c02
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82 # XCMS 3.x |
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83 if (class(xobject) == "XCMSnExp") { |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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84 # Get the legacy xcmsSet object |
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85 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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86 sampclass(xset) <- xset@phenoData$sample_group |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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87 return (xset) |
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88 } |
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89 } |
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90 |
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91 # Requires |
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92 pa <- loadRData(opt$pa, 'pa') |
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93 xset <- loadRData(opt$xset, c('xset','xdata')) |
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94 xset <- getxcmsSetObject(xset) |
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95 |
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96 pa@cores <- opt$cores |
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97 |
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98 print(pa@fileList) |
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99 print(xset@filepaths) |
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100 |
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101 if(is.null(opt$intense)){ |
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102 intense = FALSE |
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103 }else{ |
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104 intense = TRUE |
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105 } |
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106 |
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107 if(is.null(opt$convert2RawRT)){ |
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108 convert2RawRT = FALSE |
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109 }else{ |
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110 convert2RawRT= TRUE |
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111 } |
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112 |
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113 if(is.null(opt$createDB)){ |
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114 createDB = FALSE |
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115 }else{ |
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116 createDB = TRUE |
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117 } |
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118 |
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119 if(is.null(opt$useGroup)){ |
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120 fix <- xset_pa_filename_fix(opt, pa, xset) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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121 pa <- fix[[1]] |
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122 xset <- fix[[2]] |
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123 useGroup=FALSE |
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124 }else{ |
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125 # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object |
f52287a06c02
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126 print('useGroup') |
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127 fix <- xset_pa_filename_fix(opt, pa) |
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128 pa <- fix[[1]] |
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129 useGroup=TRUE |
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130 } |
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131 |
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132 |
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133 if(is.null(opt$grp_peaklist)){ |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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134 grp_peaklist = NA |
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135 }else{ |
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136 grp_peaklist = opt$grp_peaklist |
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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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137 } |
f52287a06c02
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138 print(useGroup) |
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139 |
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140 |
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141 |
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142 pa <- msPurity::frag4feature(pa=pa, |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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143 xset=xset, |
f52287a06c02
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144 ppm=opt$ppm, |
f52287a06c02
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145 plim=opt$plim, |
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146 intense=intense, |
f52287a06c02
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147 convert2RawRT=convert2RawRT, |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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148 db_name='alldata.sqlite', |
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149 out_dir=opt$out_dir, |
f52287a06c02
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150 grp_peaklist=grp_peaklist, |
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151 create_db=createDB, |
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152 use_group=useGroup) |
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153 |
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154 print(pa) |
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155 save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData')) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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156 |
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157 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) |
f52287a06c02
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158 |
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159 print(head(pa@grped_df)) |
f52287a06c02
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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160 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t') |