Mercurial > repos > recetox > ramclustr

annotate 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
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cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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1 store_output <- function(
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2 ramclustr_obj,
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3 output_filename,
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4 output_method_metadata,
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5 output_merge_msp,
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6 output_spec_abundance) {
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7 save(ramclustr_obj, file = output_filename)
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8 RAMClustR::write.methods(ramclustr_obj, output_method_metadata)
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9 RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp)
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10 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
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11 }
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12
4
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13 load_experiment_definition <- function(filename) {
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14 experiment <- RAMClustR::defineExperiment(csv = filename)
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15 return(experiment)
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16 }
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17
0
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18 read_metadata <- function(filename) {
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19 data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
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20
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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21 if (!"qc" %in% colnames(data)) {
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22 if ("sampleType" %in% colnames(data)) {
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23 data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE)
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24 }
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25 }
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26
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27 if (!"order" %in% colnames(data)) {
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28 if ("injectionOrder" %in% colnames(data)) {
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29 names(data)[names(data) == "injectionOrder"] <- "order"
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30 }
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31 }
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32
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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33 return(data)
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34 }
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35
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36 ramclustr_xcms <- function(
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37 input_xcms,
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38 sr,
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39 deep_split,
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40 block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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41 mult,
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42 hmax,
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43 collapse,
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44 use_pheno,
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45 qc_inj_range,
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46 normalize,
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47 min_module_size,
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48 linkage,
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49 mzdec,
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50 cor_method,
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51 rt_only_low_n,
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52 replace_zeros,
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53 st = NULL,
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54 maxt = NULL,
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55 fftempdir = NULL,
4
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56 metadata_file = NULL,
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57 exp_design = NULL
0
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58 ) {
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59 obj <- load(input_xcms)
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60
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61 batch <- NULL
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62 order <- NULL
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63 qc <- NULL
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64
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65 if (!is.null(metadata_file)) {
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66 metadata <- read_metadata(metadata_file)
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67 batch <- metadata$batch
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68 order <- metadata$order
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69 qc <- metadata$qc
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70 }
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71
4
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72 experiment <- NULL
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73
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74 if (!is.null(exp_design)) {
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75 experiment <- load_experiment_definition(exp_design)
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76 }
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77
0
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78 x <- RAMClustR::ramclustR(
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79 xcmsObj = xdata,
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80 st = st,
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81 maxt = maxt,
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82 sr = sr,
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83 deepSplit = deep_split,
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84 blocksize = block_size,
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85 mult = mult,
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86 hmax = hmax,
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87 collapse = collapse,
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88 usePheno = use_pheno,
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89 mspout = FALSE,
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90 qc.inj.range = qc_inj_range,
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diff changeset
91 normalize = normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
92 minModuleSize = min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
93 linkage = linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
94 mzdec = mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
95 cor.method = cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
96 rt.only.low.n = rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
97 fftempdir = fftempdir,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
98 replace.zeros = replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
99 batch = batch,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
100 order = order,
4
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
101 qc = qc,
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
102 ExpDes = experiment
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
103 )
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
104 return(x)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
105 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
106
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
107 ramclustr_csv <- function(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
108 ms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
109 idmsms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
110 sample_name_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
111 feature_delimiter,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
112 retention_time_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
113 sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
114 deep_split,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
115 block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
116 mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
117 hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
118 collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
119 use_pheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
120 qc_inj_range,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
121 normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
122 min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
123 linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
124 mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
125 cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
126 rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
127 replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
128 st = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
129 maxt = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
130 fftempdir = NULL,
4
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
131 metadata_file = NULL,
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
132 exp_design = NULL
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
133 ) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
134 if (!file.exists(idmsms))
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
135 idmsms <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
136
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
137 batch <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
138 order <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
139 qc <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
140
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
141 if (!is.null(metadata_file)) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
142 metadata <- read_metadata(metadata_file)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
143 batch <- metadata$batch
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
144 order <- metadata$order
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
145 qc <- metadata$qc
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
146 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
147
4
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
148 experiment <- NULL
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
149
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
150 if (!is.null(exp_design)) {
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
151 experiment <- load_experiment_definition(exp_design)
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
152 }
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
153
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
154 x <- RAMClustR::ramclustR(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
155 ms = ms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
156 idmsms = idmsms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
157 featdelim = feature_delimiter,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
158 timepos = retention_time_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
159 sampNameCol = sample_name_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
160 st = st,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
161 maxt = maxt,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
162 sr = sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
163 deepSplit = deep_split,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
164 blocksize = block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
165 mult = mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
166 hmax = hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
167 collapse = collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
168 usePheno = use_pheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
169 mspout = FALSE,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
170 qc.inj.range = qc_inj_range,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
171 normalize = normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
172 minModuleSize = min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
173 linkage = linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
174 mzdec = mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
175 cor.method = cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
176 rt.only.low.n = rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
177 fftempdir = fftempdir,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
178 replace.zeros = replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
179 batch = batch,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
180 order = order,
4
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
181 qc = qc,
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 0
diff changeset
182 ExpDes = experiment
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
183 )
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
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184 return(x)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
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185 }