Mercurial > repos > recetox > ramclustr

comparison ramclustr_wrapper.R @ 4:69e0da4703b5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
author recetox
date Fri, 04 Feb 2022 08:31:26 +0000
parents cb0b83b330fd
children 10ded21d47c0
comparison
equal deleted inserted replaced
3:211cd88b5148 4:69e0da4703b5
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 load_experiment_definition <- function(filename) {
14 experiment <- RAMClustR::defineExperiment(csv = filename)
15 return(experiment)
11 } 16 }
12 17
13 read_metadata <- function(filename) { 18 read_metadata <- function(filename) {
14 data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE) 19 data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
15 20
46 rt_only_low_n, 51 rt_only_low_n,
47 replace_zeros, 52 replace_zeros,
48 st = NULL, 53 st = NULL,
49 maxt = NULL, 54 maxt = NULL,
50 fftempdir = NULL, 55 fftempdir = NULL,
51 metadata_file = NULL 56 metadata_file = NULL,
57 exp_design = NULL
52 ) { 58 ) {
53 obj <- load(input_xcms) 59 obj <- load(input_xcms)
54 60
55 batch <- NULL 61 batch <- NULL
56 order <- NULL 62 order <- NULL
59 if (!is.null(metadata_file)) { 65 if (!is.null(metadata_file)) {
60 metadata <- read_metadata(metadata_file) 66 metadata <- read_metadata(metadata_file)
61 batch <- metadata$batch 67 batch <- metadata$batch
62 order <- metadata$order 68 order <- metadata$order
63 qc <- metadata$qc 69 qc <- metadata$qc
70 }
71
72 experiment <- NULL
73
74 if (!is.null(exp_design)) {
75 experiment <- load_experiment_definition(exp_design)
64 } 76 }
65 77
66 x <- RAMClustR::ramclustR( 78 x <- RAMClustR::ramclustR(
67 xcmsObj = xdata, 79 xcmsObj = xdata,
68 st = st, 80 st = st,
84 rt.only.low.n = rt_only_low_n, 96 rt.only.low.n = rt_only_low_n,
85 fftempdir = fftempdir, 97 fftempdir = fftempdir,
86 replace.zeros = replace_zeros, 98 replace.zeros = replace_zeros,
87 batch = batch, 99 batch = batch,
88 order = order, 100 order = order,
89 qc = qc 101 qc = qc,
102 ExpDes = experiment
90 ) 103 )
91 return(x) 104 return(x)
92 } 105 }
93 106
94 ramclustr_csv <- function( 107 ramclustr_csv <- function(
113 rt_only_low_n, 126 rt_only_low_n,
114 replace_zeros, 127 replace_zeros,
115 st = NULL, 128 st = NULL,
116 maxt = NULL, 129 maxt = NULL,
117 fftempdir = NULL, 130 fftempdir = NULL,
118 metadata_file = NULL 131 metadata_file = NULL,
132 exp_design = NULL
119 ) { 133 ) {
120 if (!file.exists(idmsms)) 134 if (!file.exists(idmsms))
121 idmsms <- NULL 135 idmsms <- NULL
122 136
123 batch <- NULL 137 batch <- NULL
127 if (!is.null(metadata_file)) { 141 if (!is.null(metadata_file)) {
128 metadata <- read_metadata(metadata_file) 142 metadata <- read_metadata(metadata_file)
129 batch <- metadata$batch 143 batch <- metadata$batch
130 order <- metadata$order 144 order <- metadata$order
131 qc <- metadata$qc 145 qc <- metadata$qc
146 }
147
148 experiment <- NULL
149
150 if (!is.null(exp_design)) {
151 experiment <- load_experiment_definition(exp_design)
132 } 152 }
133 153
134 x <- RAMClustR::ramclustR( 154 x <- RAMClustR::ramclustR(
135 ms = ms, 155 ms = ms,
136 idmsms = idmsms, 156 idmsms = idmsms,
156 rt.only.low.n = rt_only_low_n, 176 rt.only.low.n = rt_only_low_n,
157 fftempdir = fftempdir, 177 fftempdir = fftempdir,
158 replace.zeros = replace_zeros, 178 replace.zeros = replace_zeros,
159 batch = batch, 179 batch = batch,
160 order = order, 180 order = order,
161 qc = qc 181 qc = qc,
182 ExpDes = experiment
162 ) 183 )
163 return(x) 184 return(x)
164 } 185 }