changeset 3:6b0fef8a77c0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit bc3445f7c41271b0062c7674108f57708d08dd28

--- a/isolib.R	Wed Apr 24 14:51:32 2024 +0000
+++ b/isolib.R	Thu May 30 14:52:02 2024 +0000
@@ -6,77 +6,77 @@
 
 #' @param args A list of command line arguments.
 main <- function() {
-  data(isotopes)
-  data(adducts)
+    data(isotopes)
+    data(adducts)
+
+    args <- commandArgs(trailingOnly = TRUE)
+    compound_table <- read_tsv(
+        file = args[1],
+        col_types = "ccd",
+        col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt")
+    )
+    adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE)))
+
+    chemforms <- compound_table$formula
+    chemforms <- check_chemform(isotopes, chemforms)[, 2]
 
-  args <- commandArgs(trailingOnly = TRUE)
-  compound_table <- read_tsv(
-    file = args[1],
-    col_types = "ccd",
-    col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt")
-  )
-  adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE)))
+    spectra <- data.frame()
+
+    for (current in adducts_to_use) {
+        adduct <- adducts[adducts$Name == current, ]
+        multiplied_chemforms <- multiform(chemforms, adduct$Mult)
 
-  chemforms <- compound_table$formula
-  chemforms <- check_chemform(isotopes, chemforms)[, 2]
+        if (adduct$Ion_mode == "negative") {
+            merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
+        } else {
+            merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
+        }
 
-  spectra <- data.frame()
+        charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
+        adduct_string <- paste0("[", adduct$Name, "]", charge_string)
+        precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass
 
-  for (current in adducts_to_use) {
-    adduct <- adducts[adducts$Name == current, ]
-    multiplied_chemforms <- multiform(chemforms, adduct$Mult)
+        if (args[4] == TRUE) {
+            names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
+        } else {
+            names <- compound_table$name
+        }
+
+        spectra_df <- data.frame(
+            name = names,
+            adduct = adduct_string,
+            formula = chemforms,
+            charge = adduct$Charge,
+            ionization_mode = adduct$Ion_mode,
+            precursor_mz = precursor_mz,
+            msLevel = as.integer(1)
+        )
 
-    if (adduct$Ion_mode == "negative") {
-      merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
-    } else {
-      merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
-    }
+        if ("rt" %in% colnames(compound_table)) {
+            spectra_df$retention_time <- compound_table$rt
+        }
+
+        patterns <- enviPat::isopattern(
+            isotopes = isotopes,
+            chemforms = merged_chemforms,
+            charge = adduct$Charge,
+            threshold = as.numeric(args[3]),
+        )
 
-    charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
-    adduct_string <- paste0("[", adduct$Name, "]", charge_string)
-    precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass
+        mzs <- list()
+        intensities <- list()
+        for (i in seq_along(patterns)) {
+            mzs <- append(mzs, list(patterns[[i]][, 1]))
+            intensities <- append(intensities, list(patterns[[i]][, 2]))
+        }
 
-    if (args[4] == TRUE) {
-      names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
-    } else {
-      names <- compound_table$name
+        spectra_df$mz <- mzs
+        spectra_df$intensity <- intensities
+        spectra <- rbind(spectra, spectra_df)
     }
 
-    spectra_df <- data.frame(
-      name = names,
-      adduct = adduct_string,
-      formula = chemforms,
-      charge = adduct$Charge,
-      ionization_mode = adduct$Ion_mode,
-      precursor_mz = precursor_mz,
-      msLevel = as.integer(1)
-    )
-
-    if ("rt" %in% colnames(compound_table)) {
-      spectra_df$retention_time <- compound_table$rt
-    }
-
-    patterns <- enviPat::isopattern(
-      isotopes = isotopes,
-      chemforms = merged_chemforms,
-      charge = adduct$Charge,
-      threshold = as.numeric(args[3]),
-    )
-
-    mzs <- list()
-    intensities <- list()
-    for (i in seq_along(patterns)) {
-      mzs <- append(mzs, list(patterns[[i]][, 1]))
-      intensities <- append(intensities, list(patterns[[i]][, 2]))
-    }
-
-    spectra_df$mz <- mzs
-    spectra_df$intensity <- intensities
-    spectra <- rbind(spectra, spectra_df)
-  }
-
-  sps <- Spectra(spectra)
-  export(sps, MsBackendMsp(), file = args[5])
+    sps <- Spectra(spectra)
+    export(sps, MsBackendMsp(), file = args[5])
 }
 
 # Get the command line arguments