Mercurial > repos > tomnl > mspurity_combineannotations

annotate createDatabase.R @ 2:e912634293f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
author tomnl
date Fri, 14 Jun 2019 09:10:43 -0400
parents d6350a637d4a
children b22aa0a9fc25
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
1 library(msPurity)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
2 library(optparse)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
3 library(xcms)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
4 library(CAMERA)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
5 print(sessionInfo())
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
6 print('CREATING DATABASE')
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
7
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
8
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
9
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
10 xset_pa_filename_fix <- function(opt, pa, xset){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
11
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
15
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
17 filepaths <- filepaths[filepaths != ""]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
18 new_names <- basename(filepaths)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
19
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
21 galaxy_names <- galaxy_names[galaxy_names != ""]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
22
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
23 nsave <- names(pa@fileList)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
24 old_filenames <- basename(pa@fileList)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
26 names(pa@fileList) <- nsave
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
27
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
30 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
31
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
32
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
35 print('FILELISTS DO NOT MATCH')
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
36 message('FILELISTS DO NOT MATCH')
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
37 quit(status = 1)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
38 }else{
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
39 xset@filepaths <- unname(pa@fileList)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
40 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
41 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
42
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
43 print(xset@phenoData)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
44 print(xset@filepaths)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
45
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
46 return(list(pa, xset))
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
47 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
48
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
49
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
50
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
51
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
52 option_list <- list(
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
53 make_option(c("-o", "--outDir"), type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
54 make_option("--pa", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
55 make_option("--xset_xa", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
56 make_option("--xcms_camera_option", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
57 make_option("--eic", action="store_true"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
58 make_option("--cores", default=4),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
59 make_option("--mzML_files", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
60 make_option("--galaxy_names", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
61 make_option("--grpPeaklist", type="character"),
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
62 make_option("--raw_rt_columns", action="store_true")
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
63 )
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
64
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
65
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
66 # store options
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
67 opt<- parse_args(OptionParser(option_list=option_list))
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
68 print(opt)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
69
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
70 loadRData <- function(rdata_path, name){
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
71 #loads an RData file, and returns the named xset object if it is there
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
72 load(rdata_path)
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
73 return(get(ls()[ls() %in% name]))
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
74 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
75
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
76 getxcmsSetObject <- function(xobject) {
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
77 # XCMS 1.x
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
78 if (class(xobject) == "xcmsSet")
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
79 return (xobject)
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
80 # XCMS 3.x
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
81 if (class(xobject) == "XCMSnExp") {
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
82 # Get the legacy xcmsSet object
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
83 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
84 sampclass(xset) <- xset@phenoData$sample_group
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
85 return (xset)
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
86 }
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
87 }
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
88
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
89
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
90 print(paste('pa', opt$pa))
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
91 print(opt$xset)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
92
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
93 print(opt$xcms_camera_option)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
94 # Requires
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
95 pa <- loadRData(opt$pa, 'pa')
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
96
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
97
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
98 print(pa@fileList)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
99
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
100
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
101
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
102 if (opt$xcms_camera_option=='xcms'){
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
103
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
104 xset <- loadRData(opt$xset, c('xset','xdata'))
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
105 xset <- getxcmsSetObject(xset)
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
106 fix <- xset_pa_filename_fix(opt, pa, xset)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
107 pa <- fix[[1]]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
108 xset <- fix[[2]]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
109 xa <- NULL
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
110 }else{
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
111
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
112 xa <- loadRData(opt$xset, 'xa')
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
113 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
114 pa <- fix[[1]]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
115 xa@xcmsSet <- fix[[2]]
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
116 xset <- NULL
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
117 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
118
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
119
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
120
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
121 if(is.null(opt$grp_peaklist)){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
122 grpPeaklist = NA
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
123 }else{
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
124 grpPeaklist = opt$grp_peaklist
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
125 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
126
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
127
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
128
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
129 dbPth <- msPurity::createDatabase(pa,
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
130 xset=xset,
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
131 xsa=xa,
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
132 outDir=opt$outDir,
2
e912634293f5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7c8cb8294e711ca45f19de7bd9564157527f98db
tomnl
parents: 0
diff changeset
133 grpPeaklist=grpPeaklist,
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
134 dbName='createDatabase_output.sqlite'
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
135 )
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
136
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
137
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
138
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
139 if (!is.null(opt$eic)){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
140 if (is.null(opt$raw_rt_columns)){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
141 rtrawColumns <- FALSE
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
142 }else{
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
143 rtrawColumns <- TRUE
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
144 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
145 if (is.null(xset)){
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
146 xset <- xa@xcmsSet
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
147 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
148 # previous check should have matched filelists together
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
149 xset@filepaths <- unname(pa@fileList)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
150
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
151 # Saves the EICS into the previously created database
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
152 px <- msPurity::purityX(xset, saveEIC = TRUE,
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
153 cores=1, sqlitePth=db_pth,
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
154 rtrawColumns = rtrawColumns)
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
155 }
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
156
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
157 con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)