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annotate createMSP.R @ 0:ca0ac330f1a4 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:13:42 -0400
parents
children 2c8b5a640a04
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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1 library(optparse)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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2 library(msPurity)
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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3 print(sessionInfo())
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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5 # Get the parameter
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6 option_list <- list(
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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7 make_option(c("-i","--rdata_input"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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8 make_option(c("-m","--method"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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9 make_option(c("-meta","--metadata"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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10 make_option(c("-metac","--metadata_cols"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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11 make_option(c("-a","--adduct_split"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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12 make_option(c("-x","--xcms_groupids"),type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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13 make_option(c("-f","--filter"),action="store_true"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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14 make_option("--intensity_ra",type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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15 make_option("--msp_schema",type="character"),
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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16 make_option(c("-o","--out_dir"),type="character", default=".")
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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17 )
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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18 opt <- parse_args(OptionParser(option_list=option_list))
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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20 print(opt)
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22 load(opt$rdata_input)
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24 if (is.null(opt$metadata)){
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25 metadata <- NULL
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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26 }else{
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27 metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE)
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28 print(head(metadata))
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29 }
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31 if(is.null(opt$adduct_split)){
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32 adduct_split <- FALSE
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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33 }else{
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34 adduct_split <- TRUE
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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35 }
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37 if (is.null(opt$xcms_groupids)){
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38 xcms_groupids <- NULL
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39 }else{
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40 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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41 }
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43 if(is.null(opt$filter)){
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44 filter <- FALSE
ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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45 }else{
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46 filter <- TRUE
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47 }
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49 msPurity::createMSP(pa,
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50 msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'),
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51 metadata = metadata,
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52 metadata_cols = opt$metadata_cols,
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53 method = opt$method,
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54 adduct_split = adduct_split,
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55 xcms_groupids = xcms_groupids,
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56 filter = filter,
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57 intensity_ra=opt$intensity_ra,
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58 msp_schema=opt$msp_schema)
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59
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60 print('msp created')