Mercurial > repos > recetox > ramclustr

annotate ramclustr_wrapper.R @ 1:15e173c5762c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
author recetox
date Thu, 19 Aug 2021 07:17:15 +0000
parents cb0b83b330fd
children 69e0da4703b5
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cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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diff changeset
1 store_output <- function(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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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,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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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)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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10 write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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11 }
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12
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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13 read_metadata <- function(filename) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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14 data <- read.csv(filename, header = TRUE, stringsAsFactors = FALSE)
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15
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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16 if (!"qc" %in% colnames(data)) {
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17 if ("sampleType" %in% colnames(data)) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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18 data$qc <- ifelse(data$sampleType == "qc", TRUE, FALSE)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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19 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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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
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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22 if (!"order" %in% colnames(data)) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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23 if ("injectionOrder" %in% colnames(data)) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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24 names(data)[names(data) == "injectionOrder"] <- "order"
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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25 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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26 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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27
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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28 return(data)
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29 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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30
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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31 ramclustr_xcms <- function(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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32 input_xcms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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33 sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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34 deep_split,
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35 block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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36 mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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37 hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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38 collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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39 use_pheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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40 qc_inj_range,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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41 normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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42 min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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43 linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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44 mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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45 cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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46 rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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47 replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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48 st = NULL,
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49 maxt = NULL,
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50 fftempdir = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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51 metadata_file = NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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52 ) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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53 obj <- load(input_xcms)
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54
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55 batch <- NULL
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56 order <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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57 qc <- NULL
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58
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59 if (!is.null(metadata_file)) {
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60 metadata <- read_metadata(metadata_file)
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61 batch <- metadata$batch
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62 order <- metadata$order
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63 qc <- metadata$qc
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64 }
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65
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66 x <- RAMClustR::ramclustR(
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67 xcmsObj = xdata,
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68 st = st,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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69 maxt = maxt,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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70 sr = sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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71 deepSplit = deep_split,
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72 blocksize = block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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73 mult = mult,
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74 hmax = hmax,
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75 collapse = collapse,
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76 usePheno = use_pheno,
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77 mspout = FALSE,
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78 qc.inj.range = qc_inj_range,
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79 normalize = normalize,
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80 minModuleSize = min_module_size,
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81 linkage = linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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82 mzdec = mzdec,
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83 cor.method = cor_method,
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84 rt.only.low.n = rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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85 fftempdir = fftempdir,
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86 replace.zeros = replace_zeros,
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87 batch = batch,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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88 order = order,
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89 qc = qc
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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90 )
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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diff changeset
91 return(x)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
92 }
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
93
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
94 ramclustr_csv <- function(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
95 ms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
96 idmsms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
97 sample_name_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
98 feature_delimiter,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
99 retention_time_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
100 sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
101 deep_split,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
102 block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
103 mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
104 hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
105 collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
106 use_pheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
107 qc_inj_range,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
108 normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
109 min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
110 linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
111 mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
112 cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
113 rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
114 replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
115 st = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
116 maxt = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
117 fftempdir = NULL,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
118 metadata_file = NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
119 ) {
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
120 if (!file.exists(idmsms))
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
121 idmsms <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
122
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
123 batch <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
124 order <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
125 qc <- NULL
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
126
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
127 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
128 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
129 batch <- metadata$batch
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
130 order <- metadata$order
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
131 qc <- metadata$qc
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
132 }
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 x <- RAMClustR::ramclustR(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
135 ms = ms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
136 idmsms = idmsms,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
137 featdelim = feature_delimiter,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
138 timepos = retention_time_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
139 sampNameCol = sample_name_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
140 st = st,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
141 maxt = maxt,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
142 sr = sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
143 deepSplit = deep_split,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
144 blocksize = block_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
145 mult = mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
146 hmax = hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
147 collapse = collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
148 usePheno = use_pheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
149 mspout = FALSE,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
150 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
151 normalize = normalize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
152 minModuleSize = min_module_size,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
153 linkage = linkage,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
154 mzdec = mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
155 cor.method = cor_method,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
156 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
157 fftempdir = fftempdir,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
158 replace.zeros = replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
159 batch = batch,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
160 order = order,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
161 qc = qc
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
162 )
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
163 return(x)
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
164 }