fix: psg_list (findAdducts) and sample (xsAnnotate)

nSlaves issue with findAdducts. Use of 'xcmsClusterApply' is deprecated! Use 'BPPARAM' arguments instead. Need update of the package CAMERA to parallelize. nSlaves is set by default to 1.

tools/camera/CAMERA_findAdducts.R

@@ -37,6 +37,20 @@ for (arg in names(args)) {
   args[[arg]] <- convertNullString(args[[arg]])
 }
 
+# Function to convert string to numeric lists
+convertStringToNumeric <- function(x) {
+  if (x == NULL) {
+    return(x)
+  } else {
+    # Convert string representation of a list to a numeric vector
+    # Use a regular expression to split by common separators
+    return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
+  }
+}
+
+# Convert only the 'psg_list' element in args
+args$psg_list <- convertStringToNumeric(args$psg_list)
+
 print("Argument types:")
 print(sapply(args, class))
 

tools/camera/CAMERA_groupFWHM.R

@@ -25,18 +25,19 @@ cat("\n\n")
 print("Arguments retrieved from the command line:")
 print(args)
 
-# Function to convert "NA" strings to actual NA values
-convertNAString <- function(x) {
-  if (is.vector(x)) {
-    x[x == "NA"] <- NA
-  } else if (x == "NA") {
-    x <- NA
+# Function to convert "NA" strings to actual NA values and string to numeric lists
+convertStringToNumeric <- function(x) {
+  if (x == "NA") {
+    return(NA)
+  } else {
+    # Convert string representation of a list to a numeric vector
+    # Use a regular expression to split by common separators
+    return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
   }
-  return(x)
 }
 
 # Convert only the 'sample' element in args
-args$sample <- convertNAString(args$sample)
+args$sample <- convertStringToNumeric(args$sample)
 
 print("Argument types:")
 print(sapply(args, class))

tools/camera/findAdducts.xml

@@ -103,7 +103,7 @@
                 </conditional>
             </when>
         </conditional>
-        <param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
         <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
         <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
         <expand macro="input_file_load"/>

tools/camera/findIsotopes.xml

@@ -43,7 +43,7 @@
         </param>
         <param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" />
         <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Should C12/C13 filter be applied" />
-        <param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
         <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
         <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
         <expand macro="input_file_load"/>

tools/camera/groupCorr.xml

@@ -51,9 +51,9 @@
                 <option value="maxf">maxf</option>
             <option value="area">area</option> -->
         </param>
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
         <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
         <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
-        <param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
         <expand macro="input_file_load"/>
     </inputs>
     <outputs>

tools/camera/groupFWHM.xml

@@ -28,7 +28,7 @@
             nSlaves 1
         #else
             sample $sample
-            nSlaves $nSlaves
+            nSlaves 1
         #end if
 
         @COMMAND_FILE_LOAD@
@@ -59,10 +59,11 @@
             </when>
             <when value="TRUE">
                 <param name="sample" type="text" value="NA" label="use all the samples (automatic selection)" optional="true" />
-                <param name="nSlaves" type="integer" value="1" max="3" min="1" label="for parallel mode set nSlaves higher than 1" optional="true" />
+                <!-- issue with findAdducts Use of 'xcmsClusterApply' is deprecated! Use 'BPPARAM' arguments instead. Need update of the package -->
+                <!-- <param name="nSlaves" type="integer" value="1" max="3" min="1" label="for parallel mode set nSlaves higher than 1" optional="true" /> -->
             </when>
         </conditional>
-        <param name="convertRTMinute" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
+        <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
         <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
         <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
         <expand macro="input_file_load"/>