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comparison waveica_wrapper.R @ 1:2bcfd5b450bb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit c52cdb1ab3c4e65ce3b55e29739f16abb8bfd6eb"
author recetox
date Wed, 28 Jul 2021 11:58:20 +0000
parents 2461d20911c9
children d08deef1eb44
comparison
equal deleted inserted replaced
0:2461d20911c9 1:2bcfd5b450bb
8 alpha, 8 alpha,
9 exclude_blanks 9 exclude_blanks
10 ) { 10 ) {
11 11
12 # get input from the Galaxy, preprocess data 12 # get input from the Galaxy, preprocess data
13 data <- read.csv(data, header = TRUE, row.names = "sample_name") 13 data <- read.csv(data, header = TRUE, row.names = "sampleName")
14 data <- preprocess_data(data) 14
15 # sort data by injection order
16 data <- data[order(data$injectionOrder, decreasing = FALSE), ]
17
18 data <- enumerate_groups(data)
15 19
16 # remove blanks from dataset 20 # remove blanks from dataset
17 if (exclude_blanks) { 21 if (exclude_blanks) {
18 data <- exclude_group(data) 22 data <- exclude_group(data)
19 } 23 }
37 41
38 return(normalized_data) 42 return(normalized_data)
39 } 43 }
40 44
41 45
42 # Sort data, set numerical values for groups 46 # Match group labels with [blank/sample/qc] and enumerate them
43 preprocess_data <- function(data) { 47 enumerate_groups <- function(data) {
44 # sort data by injection order
45 data <- data[order(data$injectionOrder, decreasing = FALSE), ]
46 48
47 data$class[data$class == "blank"] <- 0 49 data$sampleType[grepl("blank", tolower(data$sampleType))] <- 0
48 data$class[data$class == "sample"] <- 1 50 data$sampleType[grepl("sample", tolower(data$sampleType))] <- 1
49 data$class[data$class == "QC"] <- 2 51 data$sampleType[grepl("qc", tolower(data$sampleType))] <- 2
50 52
51 return(data) 53 return(data)
52 } 54 }
53 55
54 56
66 68
67 69
68 # Exclude blanks from a dataframe 70 # Exclude blanks from a dataframe
69 exclude_group <- function(data) { 71 exclude_group <- function(data) {
70 row_idx_to_exclude <- which(data$class %in% 0) 72 row_idx_to_exclude <- which(data$class %in% 0)
71 if (length(row_idx_to_exclude) > 1) { 73 if (length(row_idx_to_exclude) > 0) {
72 data_without_blanks <- data[-c(row_idx_to_exclude), ] 74 data_without_blanks <- data[-c(row_idx_to_exclude), ]
73 msg <- paste("Blank samples have been excluded from the dataframe.\n") 75 msg <- paste("Blank samples have been excluded from the dataframe.\n")
74 cat(msg) 76 cat(msg)
75 return(data_without_blanks) 77 return(data_without_blanks)
76 } 78 }