Mercurial > repos > tomnl > create_msp

annotate create_sqlite_db.R @ 4:7ae48818a229 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 97c9122c9af9ddca3a2498185ce8c7919c0df03a
author tomnl
date Tue, 08 May 2018 05:28:37 -0400
parents 4b417094bf71
children 278a7e7a84cf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
1 library(msPurity)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
2 library(optparse)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
3 library(xcms)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
4 library(CAMERA)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
5 print(sessionInfo())
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
6 print('CREATING DATABASE')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
7
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
8
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
9 xset_pa_filename_fix <- function(opt, pa, xset){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
10
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
11
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
15
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
17 filepaths <- filepaths[filepaths != ""]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
18 new_names <- basename(filepaths)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
19
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
21 galaxy_names <- galaxy_names[galaxy_names != ""]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
22
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
23 nsave <- names(pa@fileList)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
24 old_filenames <- basename(pa@fileList)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
26 names(pa@fileList) <- nsave
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
27
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
30 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
31
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
32
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
35 print('FILELISTS DO NOT MATCH')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
36 message('FILELISTS DO NOT MATCH')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
37 quit(status = 1)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
38 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
39 xset@filepaths <- unname(pa@fileList)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
40 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
41 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
42
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
43
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
44 return(list(pa, xset))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
45 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
46
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
47
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
48
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
49 option_list <- list(
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
50 make_option(c("-o", "--out_dir"), type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
51 make_option("--pa", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
52 make_option("--xset_xa", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
53 make_option("--xcms_camera_option", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
54 make_option("--eic", action="store_true"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
55 make_option("--cores", default=4),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
56 make_option("--mzML_files", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
57 make_option("--galaxy_names", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
58 make_option("--grp_peaklist", type="character"),
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
59 make_option("--db_name", type="character", default='lcms_data.sqlite'),
4
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
60 make_option("--raw_rt_columns", action="store_true"),
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
61 make_option("--metfrag_result", type="character"),
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
62 make_option("--sirius_csifingerid_result", type="character"),
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
63 make_option("--probmetab_result", type="character")
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
64 )
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
65
4
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
66
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
67 # store options
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
68 opt<- parse_args(OptionParser(option_list=option_list))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
69
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
70 loadRData <- function(rdata_path, name){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
71 #loads an RData file, and returns the named xset object if it is there
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
72 load(rdata_path)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
73 return(get(ls()[ls() == name]))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
74 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
75
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
76 print(paste('pa', opt$pa))
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
77 print(opt$xset)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
78 print(opt$xcms_camera_option)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
79 # Requires
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
80 pa <- loadRData(opt$pa, 'pa')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
81
4
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
82
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
83 print(pa@fileList)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
84
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
85
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
86 if (opt$xcms_camera_option=='xcms'){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
87 xset <- loadRData(opt$xset, 'xset')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
88 fix <- xset_pa_filename_fix(opt, pa, xset)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
89 pa <- fix[[1]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
90 xset <- fix[[2]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
91 xa <- NULL
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
92 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
93
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
94 xa <- loadRData(opt$xset, 'xa')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
95 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
96 pa <- fix[[1]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
97 xa@xcmsSet <- fix[[2]]
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
98 xset <- NULL
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
99 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
100
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
101
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
102
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
103
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
104
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
105 if(is.null(opt$grp_peaklist)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
106 grp_peaklist = NA
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
107 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
108 grp_peaklist = opt$grp_peaklist
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
109 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
110
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
111
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
112 print(pa@fileList)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
113 print(xset@filepaths)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
114
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
115
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
116 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
117 grp_peaklist=grp_peaklist, db_name=opt$db_name)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
118
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
119
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
120 if (!is.null(opt$eic)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
121 if (is.null(opt$raw_rt_columns)){
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
122 rtrawColumns <- FALSE
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
123 }else{
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
124 rtrawColumns <- TRUE
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
125 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
126
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
127 # Saves the EICS into the previously created database
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
128 px <- msPurity::purityX(xset, saveEIC = TRUE,
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
129 cores=opt$cores, sqlitePth=db_pth,
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
130 rtrawColumns = rtrawColumns)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
131 }
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
132
4
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
133 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
134
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
135 add_extra_table_elucidation <- function(name, pth){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
136
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
137 if (!is.null(pth)){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
138
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
139 print(pth)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
140 df <- read.table(pth, header = TRUE, sep='\t', stringsAsFactors = FALSE, comment.char = "")
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
141 # bug for repeating headers
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
142 df <- df[!df$UID=='UID',]
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
143
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
144 # get peakid, an scan id
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
145 df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
146 colnames(df_ids) <- c('grp_id', 'file_id', 'peak_id')
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
147 df <- cbind(df_ids, df)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
148 # export to database
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
149
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
150
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
151 DBI::dbWriteTable(con, name=name, value=df, row.names=FALSE)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
152
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
153 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
154
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
155 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
156
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
157
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
158 add_probmetab <- function(pth){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
159 if (!is.null(pth)){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
160
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
161 df <- read.table(pth, header = TRUE, sep='\t', stringsAsFactors = FALSE, comment.char = "")
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
162 df$grp_id <- 1:nrow(df)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
163 start <- T
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
164 for (i in 1:nrow(df)){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
165
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
166 x <- df[i,]
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
167
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
168
4
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
169 if(is.na(x$proba) | x$proba =='NA'){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
170
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
171 next
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
172 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
173
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
174 mpc <- stringr::str_split(x$mpc, ';')
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
175 proba <- stringr::str_split(x$proba, ';')
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
176
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
177 for (j in 1:length(mpc[[1]])){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
178
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
179 row <- c(x$grp_id, x$propmz, mpc[[1]][j], proba[[1]][j])
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
180
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
181 if (start){
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
182 df_out <- data.frame(t(row), stringsAsFactors=F)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
183 start <- F
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
184 }else{
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
185 df_out <- data.frame(rbind(df_out, row), stringsAsFactors=F)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
186 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
187 print(df_out)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
188
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
189 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
190
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
191 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
192
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
193 colnames(df_out) <- c('grp_id', 'propmz', 'mpc', 'proba')
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
194 DBI::dbWriteTable(con, name='probmetab_results', value=df_out, row.names=FALSE)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
195
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
196 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
197
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
198
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
199 }
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
200
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
201 add_extra_table_elucidation('metfrag_results', opt$metfrag_result)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
202 add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
203 add_probmetab(opt$probmetab_result)
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
204
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
205
7ae48818a229 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 97c9122c9af9ddca3a2498185ce8c7919c0df03a
tomnl
parents: 0
diff changeset
206
0
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
207
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
208 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
209 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
210 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
211 'FROM c_peak_groups AS cpg ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
212 'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
213 'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
214 'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
215 'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
216 'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
217
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
218 print(cmd)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
219 cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
220
4b417094bf71 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
tomnl
parents:
diff changeset
221 write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')