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comparison frag4feature.R @ 0:fe7d7cc95ca5 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Tue, 27 Mar 2018 06:03:50 -0400
parents
children 1a88758357ed
comparison
equal deleted inserted replaced
-1:000000000000 0:fe7d7cc95ca5
1 library(optparse)
2 library(msPurity)
3 library(xcms)
4
5 xset_pa_filename_fix <- function(opt, pa, xset){
6
7
8 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
9 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
10 # needs to be done due to Galaxy moving the files around and screwing up any links to files
11
12 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
13 filepaths <- filepaths[filepaths != ""]
14 new_names <- basename(filepaths)
15
16 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
17 galaxy_names <- galaxy_names[galaxy_names != ""]
18
19 nsave <- names(pa@fileList)
20 old_filenames <- basename(pa@fileList)
21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
22 names(pa@fileList) <- nsave
23
24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
26 }
27
28
29 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
30 if(!all(names(pa@fileList)==basename(xset@filepaths))){
31 print('FILELISTS DO NOT MATCH')
32 message('FILELISTS DO NOT MATCH')
33 quit(status = 1)
34 }else{
35 xset@filepaths <- unname(pa@fileList)
36 }
37 }
38
39
40 return(list(pa, xset))
41 }
42
43
44 option_list <- list(
45 make_option(c("-o", "--out_dir"), type="character"),
46 make_option("--pa", type="character"),
47 make_option("--xset", type="character"),
48 make_option("--ppm", default=10),
49 make_option("--plim", default=0.0),
50 make_option("--convert2RawRT", action="store_true"),
51 make_option("--mostIntense", action="store_true"),
52 make_option("--createDB", action="store_true"),
53 make_option("--cores", default=4),
54 make_option("--mzML_files", type="character"),
55 make_option("--galaxy_names", type="character"),
56 make_option("--grp_peaklist", type="character")
57 )
58
59 # store options
60 opt<- parse_args(OptionParser(option_list=option_list))
61
62 loadRData <- function(rdata_path, name){
63 #loads an RData file, and returns the named xset object if it is there
64 load(rdata_path)
65 return(get(ls()[ls() == name]))
66 }
67
68 # Requires
69 pa <- loadRData(opt$pa, 'pa')
70 xset <- loadRData(opt$xset, 'xset')
71
72 pa@cores <- opt$cores
73
74 print(pa@fileList)
75 print(xset@filepaths)
76
77 if(is.null(opt$mostIntense)){
78 mostIntense = FALSE
79 }else{
80 mostIntense = TRUE
81 }
82
83 if(is.null(opt$convert2RawRT)){
84 convert2RawRT = FALSE
85 }else{
86 convert2RawRT= TRUE
87 }
88
89 if(is.null(opt$createDB)){
90 createDB = FALSE
91 }else{
92 createDB = TRUE
93 }
94
95
96 fix <- xset_pa_filename_fix(opt, pa, xset)
97 pa <- fix[[1]]
98 xset <- fix[[2]]
99
100 if(is.null(opt$grp_peaklist)){
101 grp_peaklist = NA
102
103
104 }else{
105 grp_peaklist = opt$grp_peaklist
106 }
107
108 print('heck')
109 print(pa@fileList)
110 print(names(pa@fileList))
111 print(xset@filepaths)
112 saveRDS(pa, 'test_pa.rds')
113
114 pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
115 intense=opt$mostIntense, convert2RawRT=convert2RawRT,
116 db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
117 create_db=createDB)
118
119 save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
120
121 print(head(pa@grped_df))
122 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')