Mercurial > repos > recetox > ramclustr_xcms

comparison ramclustr_wrapper.R @ 3:405c8f8dc073 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:12:58 +0000
parents 8f4d04ad4acd
children
comparison
equal deleted inserted replaced
2:e46e0a0c13ca 3:405c8f8dc073
6 output_spec_abundance) { 6 output_spec_abundance) {
7 save(ramclustr_obj, file = output_filename) 7 save(ramclustr_obj, file = output_filename)
8 RAMClustR::write.methods(ramclustr_obj, output_method_metadata) 8 RAMClustR::write.methods(ramclustr_obj, output_method_metadata)
9 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp) 9 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
10 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE) 10 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
11 }
12
13 read_metadata <- function(filename) {
14 data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
15
16 if (!"qc" %in% colnames(data)) {
17 if ("sampleType" %in% colnames(data)) {
18 data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE)
19 }
20 }
21
22 if (!"order" %in% colnames(data)) {
23 if ("injectionOrder" %in% colnames(data)) {
24 names(data)[names(data) == "injectionOrder"] <- "order"
25 }
26 }
27
28 return(data)
11 } 29 }
12 30
13 ramclustr_xcms <- function( 31 ramclustr_xcms <- function(
14 input_xcms, 32 input_xcms,
15 sr, 33 sr,
27 cor_method, 45 cor_method,
28 rt_only_low_n, 46 rt_only_low_n,
29 replace_zeros, 47 replace_zeros,
30 st = NULL, 48 st = NULL,
31 maxt = NULL, 49 maxt = NULL,
32 fftempdir = NULL 50 fftempdir = NULL,
51 metadata_file = NULL
33 ) { 52 ) {
34 obj <- load(input_xcms) 53 obj <- load(input_xcms)
54
55 batch <- NULL
56 order <- NULL
57 qc <- NULL
58
59 if (!is.null(metadata_file)) {
60 metadata <- read_metadata(metadata_file)
61 batch <- metadata$batch
62 order <- metadata$order
63 qc <- metadata$qc
64 }
35 65
36 x <- RAMClustR::ramclustR( 66 x <- RAMClustR::ramclustR(
37 xcmsObj = xdata, 67 xcmsObj = xdata,
38 st = st, 68 st = st,
39 maxt = maxt, 69 maxt = maxt,
51 linkage = linkage, 81 linkage = linkage,
52 mzdec = mzdec, 82 mzdec = mzdec,
53 cor.method = cor_method, 83 cor.method = cor_method,
54 rt.only.low.n = rt_only_low_n, 84 rt.only.low.n = rt_only_low_n,
55 fftempdir = fftempdir, 85 fftempdir = fftempdir,
56 replace.zeros = replace_zeros 86 replace.zeros = replace_zeros,
87 batch = batch,
88 order = order,
89 qc = qc
57 ) 90 )
58 return(x) 91 return(x)
59 } 92 }
60 93
61 ramclustr_csv <- function( 94 ramclustr_csv <- function(
79 cor_method, 112 cor_method,
80 rt_only_low_n, 113 rt_only_low_n,
81 replace_zeros, 114 replace_zeros,
82 st = NULL, 115 st = NULL,
83 maxt = NULL, 116 maxt = NULL,
84 fftempdir = NULL 117 fftempdir = NULL,
118 metadata_file = NULL
85 ) { 119 ) {
86 if (!file.exists(idmsms)) 120 if (!file.exists(idmsms))
87 idmsms <- NULL 121 idmsms <- NULL
122
123 batch <- NULL
124 order <- NULL
125 qc <- NULL
126
127 if (!is.null(metadata_file)) {
128 metadata <- read_metadata(metadata_file)
129 batch <- metadata$batch
130 order <- metadata$order
131 qc <- metadata$qc
132 }
88 133
89 x <- RAMClustR::ramclustR( 134 x <- RAMClustR::ramclustR(
90 ms = ms, 135 ms = ms,
91 idmsms = idmsms, 136 idmsms = idmsms,
92 featdelim = feature_delimiter, 137 featdelim = feature_delimiter,
108 linkage = linkage, 153 linkage = linkage,
109 mzdec = mzdec, 154 mzdec = mzdec,
110 cor.method = cor_method, 155 cor.method = cor_method,
111 rt.only.low.n = rt_only_low_n, 156 rt.only.low.n = rt_only_low_n,
112 fftempdir = fftempdir, 157 fftempdir = fftempdir,
113 replace.zeros = replace_zeros 158 replace.zeros = replace_zeros,
159 batch = batch,
160 order = order,
161 qc = qc
114 ) 162 )
115 return(x) 163 return(x)
116 } 164 }