Mercurial > repos > tomnl > submit_to_mogi

annotate create_sqlite_db.R @ 6:187641a876b9 draft default tip

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 1800a3818988f21ef129e500818c9a087fce5875-dirty
author tomnl
date Tue, 28 Aug 2018 07:40:50 -0400
parents ac12e2f9df86
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
1 library(msPurity)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
2 library(optparse)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
3 library(xcms)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
4 library(CAMERA)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
5 print(sessionInfo())
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
6 print('CREATING DATABASE')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
7
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
8
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
9 xset_pa_filename_fix <- function(opt, pa, xset){
1
ac12e2f9df86 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
tomnl
parents: 0
diff changeset
10 print(xset@filepaths)
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
11
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
15
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
17 filepaths <- filepaths[filepaths != ""]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
18 new_names <- basename(filepaths)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
19
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
21 galaxy_names <- galaxy_names[galaxy_names != ""]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
22
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
23 nsave <- names(pa@fileList)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
24 old_filenames <- basename(pa@fileList)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
26 names(pa@fileList) <- nsave
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
27
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
30 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
31
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
32
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
35 print('FILELISTS DO NOT MATCH')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
36 message('FILELISTS DO NOT MATCH')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
37 quit(status = 1)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
38 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
39 xset@filepaths <- unname(pa@fileList)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
40 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
41 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
42
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
43
1
ac12e2f9df86 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
tomnl
parents: 0
diff changeset
44 print(xset@phenoData)
ac12e2f9df86 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
tomnl
parents: 0
diff changeset
45 print(xset@filepaths)
ac12e2f9df86 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
tomnl
parents: 0
diff changeset
46
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
47 return(list(pa, xset))
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
48 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
49
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
50
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
51
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
52
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
53 option_list <- list(
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
54 make_option(c("-o", "--out_dir"), type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
55 make_option("--pa", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
56 make_option("--xset_xa", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
57 make_option("--xcms_camera_option", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
58 make_option("--eic", action="store_true"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
59 make_option("--cores", default=4),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
60 make_option("--mzML_files", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
61 make_option("--galaxy_names", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
62 make_option("--grp_peaklist", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
63 make_option("--db_name", type="character", default='lcms_data.sqlite'),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
64 make_option("--raw_rt_columns", action="store_true"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
65 make_option("--metfrag_result", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
66 make_option("--sirius_csifingerid_result", type="character"),
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
67 make_option("--probmetab_result", type="character")
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
68 )
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
69
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
70
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
71 # store options
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
72 opt<- parse_args(OptionParser(option_list=option_list))
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
73
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
74 loadRData <- function(rdata_path, name){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
75 #loads an RData file, and returns the named xset object if it is there
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
76 load(rdata_path)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
77 return(get(ls()[ls() == name]))
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
78 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
79
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
80 print(paste('pa', opt$pa))
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
81 print(opt$xset)
1
ac12e2f9df86 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
tomnl
parents: 0
diff changeset
82
0
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
83 print(opt$xcms_camera_option)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
84 # Requires
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
85 pa <- loadRData(opt$pa, 'pa')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
86
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
87
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
88 print(pa@fileList)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
89
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
90
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
91 if (opt$xcms_camera_option=='xcms'){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
92 xset <- loadRData(opt$xset, 'xset')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
93 fix <- xset_pa_filename_fix(opt, pa, xset)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
94 pa <- fix[[1]]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
95 xset <- fix[[2]]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
96 xa <- NULL
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
97 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
98
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
99 xa <- loadRData(opt$xset, 'xa')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
100 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
101 pa <- fix[[1]]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
102 xa@xcmsSet <- fix[[2]]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
103 xset <- NULL
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
104 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
105
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
106
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
107
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
108
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
109
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
110 if(is.null(opt$grp_peaklist)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
111 grp_peaklist = NA
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
112 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
113 grp_peaklist = opt$grp_peaklist
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
114 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
115
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
116
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
117
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
118 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
119 grp_peaklist=grp_peaklist, db_name=opt$db_name)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
120
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
121 print(db_pth)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
122
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
123 if (!is.null(opt$eic)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
124 if (is.null(opt$raw_rt_columns)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
125 rtrawColumns <- FALSE
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
126 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
127 rtrawColumns <- TRUE
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
128 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
129 if (is.null(xset)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
130 xset <- xa@xcmsSet
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
131 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
132 # previous check should have matched filelists together
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
133 xset@filepaths <- unname(pa@fileList)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
134
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
135 # Saves the EICS into the previously created database
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
136 px <- msPurity::purityX(xset, saveEIC = TRUE,
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
137 cores=1, sqlitePth=db_pth,
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
138 rtrawColumns = rtrawColumns)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
139 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
140
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
141 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
142
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
143 add_extra_table_elucidation <- function(name, pth, db_con){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
144 if (is.null(pth)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
145 return(0)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
146 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
147
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
148
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
149 DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
150
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
151
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
152 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
153
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
154 write_to_table <- function(df, db_con, name, append){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
155
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
156 df <- df[!df$UID=='UID',]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
157 print(filter_Score)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
158 print(filter_Rank)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
159 print('filter rank and score')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
160
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
161
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
162 # get peakid, an scan id
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
163 df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
164 colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
165 df <- cbind(df_ids, df)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
166 DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
167 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
168
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
169 add_probmetab <- function(pth, xset, con){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
170 if (!is.null(pth)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
171
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
172 df <- read.table(pth, header = TRUE, sep='\t', stringsAsFactors = FALSE, comment.char = "")
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
173 df$grp_id <- match(df$name, xcms::groupnames(xset))
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
174 start <- T
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
175 for (i in 1:nrow(df)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
176
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
177 x <- df[i,]
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
178
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
179
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
180 if(is.na(x$proba) | x$proba =='NA'){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
181
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
182 next
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
183 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
184
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
185 mpc <- stringr::str_split(x$mpc, ';')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
186 proba <- stringr::str_split(x$proba, ';')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
187
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
188 for (j in 1:length(mpc[[1]])){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
189
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
190 row <- c(x$grp_id, x$propmz, mpc[[1]][j], proba[[1]][j])
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
191
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
192 if (start){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
193 df_out <- data.frame(t(row), stringsAsFactors=F)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
194 start <- F
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
195 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
196 df_out <- data.frame(rbind(df_out, row), stringsAsFactors=F)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
197 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
198 print(df_out)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
199
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
200 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
201
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
202 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
203
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
204 colnames(df_out) <- c('grp_id', 'propmz', 'mpc', 'proba')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
205 DBI::dbWriteTable(con, name='probmetab_results', value=df_out, row.names=FALSE)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
206
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
207 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
208
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
209
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
210 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
211
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
212 add_extra_table_elucidation('metfrag_results', opt$metfrag_result, con)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
213 add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
214
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
215
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
216 if (is.null(xset)){
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
217 DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
218 add_probmetab(opt$probmetab_result, xa@xcmsSet, con)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
219 }else{
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
220
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
221 DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
222 add_probmetab(opt$probmetab_result, xset, con)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
223
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
224 }
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
225
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
226 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
227 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
228 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
229 'FROM c_peak_groups AS cpg ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
230 'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
231 'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
232 'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
233 'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
234 'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
235
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
236 print(cmd)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
237 cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
238
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
tomnl
parents:
diff changeset
239 write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')