comparison isolib.R @ 7:06f2d0d6d107 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit aec90552d259748822d040248a9e1265759cc198

6:f0fe957df1cc

library(Spectra)
library(MsBackendMsp)
library(MetaboCoreUtils)
library(readr)
library(tidyselect)


isotopes <- data.frame(
    element = character(),
    abundance = numeric(),
    isotope = character()

parse_args <- function() {
    args <- commandArgs(trailingOnly = TRUE)

    compound_table <- read_tsv(
        file = args[1],
        col_types = "ccd",
        col_select = all_of(c("name", "formula")) | any_of("rt")
    )
    # Handle missing or empty rel_to argument
    rel_to_value <- if (length(args) >= 8 && args[8] != "") {
        if (args[8] == "none") 0 else as.numeric(args[8])
    } else {
        0 # Default value is 0

        threshold = as.numeric(args[3]),
        append_adducts = args[4],
        append_isotopes = args[5],
        out_format = args[6],
        outfile = args[7],
        rel_to = rel_to_value
    )
    parsed
}

generate_isotope_spectra <- function(compound_table,

        spectra <- rbind(spectra, spectra_df)
    }
    spectra
}

write_to_msp <- function(spectra, file) {
    sps <- Spectra::Spectra(dplyr::select(spectra, -isotopes))
    Spectra::export(sps, MsBackendMsp::MsBackendMsp(), file = file)
}

write_to_table <- function(spectra, file, append_isotopes) {
    entries <- spectra |>
        dplyr::rowwise() |>
        dplyr::mutate(peaks = paste(unlist(mz), collapse = ";")) |>
        dplyr::mutate(isos = paste(unlist(isotopes), collapse = ";"))
    result <- tidyr::separate_longer_delim(

            ) |>
            dplyr::select(-all_of(c("formula", "isotopes"))) |>
            dplyr::rename(formula = full_formula) |>
            dplyr::relocate(formula, .after = name)
    }
    readr::write_tsv(result, file = file)
}

main <- function() {
    args <- parse_args()

        args$threshold,
        args$rel_to
    )

    if (args$out_format == "msp") {
        write_to_msp(spectra, args$outfile)
    } else if (args$out_format == "tabular") {
        write_to_table(spectra, args$outfile, args$append_isotopes)
    }
}

# Call the main function
main()

7:06f2d0d6d107

library(Spectra)
library(MsBackendMsp)
library(MetaboCoreUtils)
library(readr)
library(tidyselect)
library(stringr)
library(dplyr)

isotopes <- data.frame(
    element = character(),
    abundance = numeric(),
    isotope = character()

parse_args <- function() {
    args <- commandArgs(trailingOnly = TRUE)

    compound_table_full <- read_tsv(
        file = args[1],
        col_types = cols(
            name = col_character(),
            formula = col_character(),
            rt = col_double(),
            .default = col_guess()
        )
    )

    # Extract selected columns
    compound_table <- compound_table_full[, intersect(c("name", "formula", "rt"), colnames(compound_table_full)), drop = FALSE]

    # Extract remaining columns
    remaining_columns <- setdiff(colnames(compound_table_full), colnames(compound_table))
    remaining_data <- compound_table_full[, c("name", remaining_columns), drop = FALSE]

    # Handle missing or empty rel_to argument
    rel_to_value <- if (length(args) >= 8 && args[8] != "") {
        if (args[8] == "none") 0 else as.numeric(args[8])
    } else {
        0 # Default value is 0

        threshold = as.numeric(args[3]),
        append_adducts = args[4],
        append_isotopes = args[5],
        out_format = args[6],
        outfile = args[7],
        rel_to = rel_to_value,
        remaining_data = remaining_data
    )
    parsed
}

generate_isotope_spectra <- function(compound_table,

        spectra <- rbind(spectra, spectra_df)
    }
    spectra
}

join_remaining_data <- function(df, remaining_data) {
    if (nrow(remaining_data) > 0) {
        df <- df %>%
            dplyr::mutate(base_name = stringr::str_trim(stringr::str_remove(name, "\\s*\\([^)]*\\)$")))
        df <- dplyr::left_join(df, remaining_data, by = c("base_name" = "name"))
        df <- df %>% dplyr::select(-base_name)
    }
    df
}

write_to_msp <- function(spectra, file, remaining_data) {
    spectra <- join_remaining_data(spectra, remaining_data)
    sps <- Spectra::Spectra(dplyr::select(spectra, -isotopes))
    Spectra::export(sps, MsBackendMsp::MsBackendMsp(), file = file)
}

write_to_table <- function(spectra, file, append_isotopes, remaining_data) {
    entries <- spectra |>
        dplyr::rowwise() |>
        dplyr::mutate(peaks = paste(unlist(mz), collapse = ";")) |>
        dplyr::mutate(isos = paste(unlist(isotopes), collapse = ";"))
    result <- tidyr::separate_longer_delim(

            ) |>
            dplyr::select(-all_of(c("formula", "isotopes"))) |>
            dplyr::rename(formula = full_formula) |>
            dplyr::relocate(formula, .after = name)
    }
    result <- join_remaining_data(result, remaining_data)
    readr::write_tsv(result, file = file)
}

main <- function() {
    args <- parse_args()

        args$threshold,
        args$rel_to
    )

    if (args$out_format == "msp") {
        write_to_msp(spectra, args$outfile, args$remaining_data)
    } else if (args$out_format == "tabular") {
        write_to_table(spectra, args$outfile, args$append_isotopes, args$remaining_data)
    }
}

# Call the main function
main()