comparison isolib.R @ 6:f0fe957df1cc draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 148c6b04fff1cedd890d33e98d4fd787026a8628

5:964b4559eb1b

            intensities <- append(intensities, list(patterns[[i]][, 2]))

            # select all columns which describe the elemental composition
            # remove all 12C, 35Cl etc.
            # remove isotopes which don't occur
            compositions <- as.data.frame(patterns[[i]][, -c(1, 2)]) |>
                dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |>
                dplyr::select_if(~ !all(. == 0))

            # combine elemental composition into single string
            compositions <- compositions |>

        dplyr::rename(mz = peaks, isotopes = isos, rt = retention_time)

    if (append_isotopes) {
        result <- result |>
            dplyr::mutate(result,
                full_formula = paste0(formula, " (", isotopes, ")")
            ) |>
            dplyr::select(-all_of(c("formula", "isotopes"))) |>
            dplyr::rename(formula = full_formula) |>
            dplyr::relocate(formula, .after = name)
    }

6:f0fe957df1cc

            intensities <- append(intensities, list(patterns[[i]][, 2]))

            # select all columns which describe the elemental composition
            # remove all 12C, 35Cl etc.
            # remove isotopes which don't occur
            compositions <- as.data.frame(patterns[[i]][, -c(1, 2), drop = FALSE]) |>
                dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |>
                dplyr::select_if(~ !all(. == 0))

            # combine elemental composition into single string
            compositions <- compositions |>

        dplyr::rename(mz = peaks, isotopes = isos, rt = retention_time)

    if (append_isotopes) {
        result <- result |>
            dplyr::mutate(result,
                full_formula = ifelse(
                    is.na(isotopes) | isotopes == "",
                    formula,
                    paste0(formula, " (", isotopes, ")")
                )
            ) |>
            dplyr::select(-all_of(c("formula", "isotopes"))) |>
            dplyr::rename(formula = full_formula) |>
            dplyr::relocate(formula, .after = name)
    }