Mercurial > repos > computational-metabolomics > mspurity_createmsp

annotate averageFragSpectra.R @ 0:eeb5d343374c draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:19:07 +0000
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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diff changeset
1 library(optparse)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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2 library(msPurity)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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3 library(xcms)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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4 print(sessionInfo())
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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7 get_av_spectra <- function(x) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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9 if (length(x$av_intra) > 0) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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10 av_intra_df <- plyr::ldply(x$av_intra)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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12 if (nrow(av_intra_df) == 0) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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13 av_intra_df <- NULL
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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15 av_intra_df$method <- "intra"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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16 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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19 av_intra_df <- NULL
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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20 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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22 if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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23 av_inter_df <- NULL
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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24 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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25 av_inter_df <- x$av_inter
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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26 av_inter_df$method <- "inter"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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27 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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29 if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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30 av_all_df <- NULL
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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31 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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32 av_all_df <- x$av_all
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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33 av_all_df$method <- "all"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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34 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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36 combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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37
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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38 return(combined)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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39 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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40
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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42 option_list <- list(
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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43 make_option("--out_rdata", type = "character"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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44 make_option("--out_peaklist", type = "character"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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45 make_option("--pa", type = "character"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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46 make_option("--av_level", type = "character"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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47 make_option("--minfrac", default = 0.5),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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48 make_option("--minnum", default = 1),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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49 make_option("--ppm", default = 5.0),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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50 make_option("--snr", default = 0),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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51 make_option("--ra", default = 0),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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52 make_option("--av", default = "median", type = "character"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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53 make_option("--sumi", action = "store_true"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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54 make_option("--rmp", action = "store_true"),
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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55 make_option("--cores", default = 1)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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56 )
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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57
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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58 opt <- parse_args(OptionParser(option_list = option_list))
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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59 print(opt)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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62 load_r_data <- function(rdata_path, name) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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63 #loads an RData file, and returns the named xset object if it is there
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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64 load(rdata_path)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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65 return(get(ls()[ls() %in% name]))
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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66 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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68 # Requires
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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69 pa <- load_r_data(opt$pa, "pa")
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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70
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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71 pa@cores <- opt$cores
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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72
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73 if (is.null(opt$rmp)) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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74 rmp <- FALSE
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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75 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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76 rmp <- TRUE
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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77 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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78
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79 if (is.null(opt$sumi)) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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80 sumi <- FALSE
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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81 }else{
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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82 sumi <- TRUE
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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83 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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84
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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85 if (opt$av_level == "intra") {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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86 pa <- msPurity::averageIntraFragSpectra(pa,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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87 minfrac = opt$minfrac,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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88 minnum = opt$minnum,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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89 ppm = opt$ppm,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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90 snr = opt$snr,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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91 ra = opt$ra,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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92 av = opt$av,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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93 sumi = sumi,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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94 rmp = rmp,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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95 cores = opt$cores)
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96
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97 } else if (opt$av_level == "inter") {
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98
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99 pa <- msPurity::averageInterFragSpectra(pa,
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100 minfrac = opt$minfrac,
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101 minnum = opt$minnum,
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102 ppm = opt$ppm,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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103 snr = opt$snr,
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104 ra = opt$ra,
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105 av = opt$av,
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106 sumi = sumi,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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107 rmp = rmp,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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108 cores = opt$cores)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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109 } else if (opt$av_level == "all") {
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110
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111 pa <- msPurity::averageAllFragSpectra(pa,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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112 minfrac = opt$minfrac,
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113 minnum = opt$minnum,
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114 ppm = opt$ppm,
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115 snr = opt$snr,
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116 ra = opt$ra,
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117 av = opt$av,
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118 sumi = sumi,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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119 rmp = rmp,
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120 cores = opt$cores)
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121 }
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122
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123 print(pa)
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124 save(pa, file = opt$out_rdata)
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125
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126 if (length(pa) > 0) {
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127
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128 av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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129
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130 if (nrow(av_spectra) == 0) {
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131 message("No average spectra available")
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132 } else {
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133 colnames(av_spectra)[1] <- "grpid"
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134 av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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135
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136 if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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137 # Add some extra info (only required if av_intra or av_inter performed)
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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138 colnames(av_spectra)[2] <- "fileid"
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139 av_spectra$avid <- seq_len(nrow(av_spectra))
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140
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141 filenames <- sapply(av_spectra$fileid,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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142 function(x) names(pa@fileList)[as.integer(x)])
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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143 # filenames_galaxy <- sapply(
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144 # av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
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145
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146 av_spectra <- as.data.frame(
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147 append(av_spectra, list(filename = filenames), after = 2))
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148 }
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149
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150
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151 print(head(av_spectra))
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152 write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
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153
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154 }
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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155 }