Mercurial > repos > computational-metabolomics > mspurity_flagremove

annotate createMSP.R @ 9:da36e8bbcfbd 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 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:35:07 +0000
parents a0ee43397d1e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
1 library(optparse)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
2 library(msPurity)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
3 print(sessionInfo())
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
4
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
5 # Get the parameter
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
6 option_list <- list(
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
7 make_option("--rdata_input", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
8 make_option("--method", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
9 make_option("--metadata", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
10 make_option("--metadata_cols", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
11 make_option("--metadata_cols_filter", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
12 make_option("--adduct_split", action = "store_true"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
13 make_option("--xcms_groupids", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
14 make_option("--filter", action = "store_true"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
15 make_option("--intensity_ra", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
16 make_option("--include_adducts", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
17 make_option("--msp_schema", type = "character"),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
18 make_option("--include_adducts_custom", type = "character", default = ""),
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
19 make_option("--out_dir", type = "character", default = ".")
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
20 )
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
21 opt <- parse_args(OptionParser(option_list = option_list))
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
22
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
23 print(opt)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
24
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
25 load(opt$rdata_input)
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
26
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
27 if (is.null(opt$metadata)) {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
28 metadata <- NULL
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
29 } else {
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
30 metadata <- read.table(opt$metadata,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
31 header = TRUE, sep = "\t",
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
32 stringsAsFactors = FALSE, check.names = FALSE
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
33 )
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
34
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
35 if (!opt$metadata_cols_filter == "") {
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
36 metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ",")[[1]]
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
37
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
38 metadata <- metadata[, metadata_cols_filter, drop = FALSE]
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
39 print(metadata)
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
40
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
41 if (!"grpid" %in% colnames(metadata)) {
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
42 metadata$grpid <- seq_len(nrow(metadata))
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
43 }
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
44
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
45 print(metadata)
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
46 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
47 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
48
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
49
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
50
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
51 if (is.null(opt$metadata_cols) || opt$metadata_cols == "") {
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
52 metadata_cols <- NULL
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
53 } else {
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
54 metadata_cols <- opt$metadata_cols
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
55 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
56
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
57
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
58 if (is.null(opt$adduct_split)) {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
59 adduct_split <- FALSE
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
60 } else {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
61 adduct_split <- TRUE
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
62 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
63
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
64 if (is.null(opt$xcms_groupids)) {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
65 xcms_groupids <- NULL
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
66 } else {
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
67 xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ",")[[1]])
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
68 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
69
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
70
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
71 if (is.null(opt$include_adducts_custom)) {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
72 include_adducts_custom <- ""
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
73 } else {
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
74 include_adducts_custom <- opt$include_adducts_custom
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
75 }
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
76
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
77
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
78 if (opt$include_adducts == "None") {
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
79 include_adducts <- ""
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
80 } else {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
81 include_adducts <- opt$include_adducts
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
82 }
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
83
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
84 include_adducts_all <- paste(include_adducts_custom, ",", include_adducts, sep = "")
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
85
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
86 include_adducts_all <- gsub("^,", "", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
87 include_adducts_all <- gsub(",$", "", include_adducts_all)
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
88
3
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
89 include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
90 include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
91 include_adducts_all <- trimws(include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
92 include_adducts_all <- gsub(",", " ", include_adducts_all)
d2373ced0ded "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents: 0
diff changeset
93
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
94
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
95
6
a67b129cd78e "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 3
diff changeset
96 if (is.null(opt$filter)) {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
97 filter <- FALSE
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
98 } else {
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
99 filter <- TRUE
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
100 }
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
101
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
102
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
103
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
104 msPurity::createMSP(pa,
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
105 msp_file_pth = file.path(opt$out_dir, "lcmsms_spectra.msp"),
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
106 metadata = metadata,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
107 metadata_cols = metadata_cols,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
108 method = opt$method,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
109 adduct_split = adduct_split,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
110 xcms_groupids = xcms_groupids,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
111 filter = filter,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
112 intensity_ra = opt$intensity_ra,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
113 include_adducts = include_adducts_all,
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
114 msp_schema = opt$msp_schema
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
115 )
0
5d0461edc7fd "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
116
8
a0ee43397d1e planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 6
diff changeset
117 print("msp created")