# HG changeset patch # User recetox # Date 1751362112 0 # Node ID 06f2d0d6d107b45de6f6ad49a7ab91d487713cd8 # Parent f0fe957df1ccc9e7d3c88d42a1e8a04a236579d8 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit aec90552d259748822d040248a9e1265759cc198 diff -r f0fe957df1cc -r 06f2d0d6d107 isolib.R --- a/isolib.R Thu Jun 12 09:17:20 2025 +0000 +++ b/isolib.R Tue Jul 01 09:28:32 2025 +0000 @@ -4,7 +4,8 @@ library(MetaboCoreUtils) library(readr) library(tidyselect) - +library(stringr) +library(dplyr) isotopes <- data.frame( element = character(), @@ -33,11 +34,23 @@ parse_args <- function() { args <- commandArgs(trailingOnly = TRUE) - compound_table <- read_tsv( + compound_table_full <- read_tsv( file = args[1], - col_types = "ccd", - col_select = all_of(c("name", "formula")) | any_of("rt") + 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]) @@ -60,7 +73,8 @@ append_isotopes = args[5], out_format = args[6], outfile = args[7], - rel_to = rel_to_value + rel_to = rel_to_value, + remaining_data = remaining_data ) parsed } @@ -176,12 +190,23 @@ spectra } -write_to_msp <- function(spectra, file) { +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) { +write_to_table <- function(spectra, file, append_isotopes, remaining_data) { entries <- spectra |> dplyr::rowwise() |> dplyr::mutate(peaks = paste(unlist(mz), collapse = ";")) |> @@ -208,6 +233,7 @@ dplyr::rename(formula = full_formula) |> dplyr::relocate(formula, .after = name) } + result <- join_remaining_data(result, remaining_data) readr::write_tsv(result, file = file) } @@ -222,9 +248,9 @@ ) if (args$out_format == "msp") { - write_to_msp(spectra, args$outfile) + write_to_msp(spectra, args$outfile, args$remaining_data) } else if (args$out_format == "tabular") { - write_to_table(spectra, args$outfile, args$append_isotopes) + write_to_table(spectra, args$outfile, args$append_isotopes, args$remaining_data) } } diff -r f0fe957df1cc -r 06f2d0d6d107 isolib.xml --- a/isolib.xml Thu Jun 12 09:17:20 2025 +0000 +++ b/isolib.xml Tue Jul 01 09:28:32 2025 +0000 @@ -1,4 +1,4 @@ - + create an isotopic pattern library for given compounds and adducts based on enviPat + + + + + + + + + + + + + + + +