Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison frag4feature.R @ 0:de93f6aac760 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 12:21:39 +0000
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-1:000000000000 0:de93f6aac760
1 library(optparse)
2 library(msPurity)
3 library(xcms)
4 print(sessionInfo())
5
6 xset_pa_filename_fix <- function(opt, pa, xset=NULL) {
7
8
9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)) {
10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
12
13 filepaths <- trimws(strsplit(opt$mzML_files, ",")[[1]]) # nolint
14
15 filepaths <- filepaths[filepaths != ""]
16
17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ",")[[1]])
18 galaxy_names <- galaxy_names[galaxy_names != ""]
19
20 nsave <- names(pa@fileList)
21 old_filenames <- basename(pa@fileList)
22
23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
24 names(pa@fileList) <- nsave
25
26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
28 }
29 print(pa@fileList)
30
31 if (!is.null(xset)) {
32
33 print(xset@filepaths)
34
35 if (!all(basename(pa@fileList) == basename(xset@filepaths))) {
36 if (!all(names(pa@fileList) == basename(xset@filepaths))) {
37 print("FILELISTS DO NOT MATCH")
38 message("FILELISTS DO NOT MATCH")
39 quit(status = 1)
40 }else{
41 xset@filepaths <- unname(pa@fileList)
42 }
43 }
44 }
45
46 return(list(pa, xset))
47 }
48
49
50 option_list <- list(
51 make_option(c("-o", "--out_dir"), type = "character"),
52 make_option("--pa", type = "character"),
53 make_option("--xset", type = "character"),
54 make_option("--ppm", default = 10),
55 make_option("--plim", default = 0.0),
56 make_option("--convert2RawRT", action = "store_true"),
57 make_option("--intense", action = "store_true"),
58 make_option("--createDB", action = "store_true"),
59 make_option("--cores", default = 4),
60 make_option("--mzML_files", type = "character"),
61 make_option("--galaxy_names", type = "character"),
62 make_option("--grp_peaklist", type = "character"),
63 make_option("--useGroup", action = "store_true")
64 )
65
66 # store options
67 opt <- parse_args(OptionParser(option_list = option_list))
68 print(opt)
69
70 loadRData <- function(rdata_path, name) {
71 #loads an RData file, and returns the named xset object if it is there
72 load(rdata_path)
73 return(get(ls()[ls() %in% name]))
74 }
75
76 # This function retrieve a xset like object
77 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
78 getxcmsSetObject <- function(xobject) {
79 # XCMS 1.x
80 if (class(xobject) == "xcmsSet")
81 return(xobject)
82 # XCMS 3.x
83 if (class(xobject) == "XCMSnExp") {
84 # Get the legacy xcmsSet object
85 suppressWarnings(xset <- as(xobject, "xcmsSet"))
86 sampclass(xset) <- xset@phenoData$sample_group
87 return(xset)
88 }
89 }
90
91 # Requires
92 pa <- loadRData(opt$pa, "pa")
93 xset <- loadRData(opt$xset, c("xset", "xdata"))
94 xset <- getxcmsSetObject(xset)
95
96 pa@cores <- opt$cores
97
98 print(pa@fileList)
99 print(xset@filepaths)
100
101 if (is.null(opt$intense)) {
102 intense <- FALSE
103 }else{
104 intense <- TRUE
105 }
106
107 if (is.null(opt$convert2RawRT)) {
108 convert2RawRT <- FALSE
109 }else{
110 convert2RawRT <- TRUE
111 }
112
113 if (is.null(opt$createDB)) {
114 createDB <- FALSE
115 }else{
116 createDB <- TRUE
117 }
118
119 if (is.null(opt$useGroup)) {
120 fix <- xset_pa_filename_fix(opt, pa, xset)
121 pa <- fix[[1]]
122 xset <- fix[[2]]
123 useGroup <- FALSE
124 }else{
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
126 print("useGroup")
127 fix <- xset_pa_filename_fix(opt, pa)
128 pa <- fix[[1]]
129 useGroup <- TRUE
130 }
131
132
133 if (is.null(opt$grp_peaklist)) {
134 grp_peaklist <- NA
135 }else{
136 grp_peaklist <- opt$grp_peaklist
137 }
138 print(useGroup)
139
140 pa <- msPurity::frag4feature(pa = pa,
141 xset = xset,
142 ppm = opt$ppm,
143 plim = opt$plim,
144 intense = intense,
145 convert2RawRT = convert2RawRT,
146 db_name = "alldata.sqlite",
147 out_dir = opt$out_dir,
148 grp_peaklist = grp_peaklist,
149 create_db = createDB,
150 use_group = useGroup)
151 print(pa)
152 save(pa, file = file.path(opt$out_dir, "frag4feature_output.RData"))
153
154 pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
155
156 print(head(pa@grped_df))
157 write.table(pa@grped_df, file.path(opt$out_dir, "frag4feature_output.tsv"), row.names = FALSE, sep = "\t")