From bc9d3de5b365069d85a3900f2f0a9bfa57cd7cd7 Mon Sep 17 00:00:00 2001
From: Damien RAT <damien.rat44@gmail.com>
Date: Wed, 6 Nov 2024 15:25:49 +0100
Subject: [PATCH] Add psg_list option to groupCorr

---
 tools/camera/CAMERA_groupCorr.R | 37 ++++++++++++++++++++++++++++++++-
 tools/camera/groupCorr.xml      | 19 +++++++++++++++++
 2 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
index bb3c41bbb..4aed27bb2 100755
--- a/tools/camera/CAMERA_groupCorr.R
+++ b/tools/camera/CAMERA_groupCorr.R
@@ -25,6 +25,41 @@ cat("\n\n")
 print("Arguments retrieved from the command line:")
 print(args)
 
+# Function to convert "NULL" strings to actual NULL values
+convertNullString <- function(x) {
+  if (x == "NULL") {
+    return(NULL)
+  }
+  return(x)
+}
+
+# Function to convert string to numeric lists
+convert_psg_list <- function(x) {
+  # Check if x is NULL or has zero length before further processing
+  if (is.null(x) || length(x) == 0) {
+    return(NULL)
+  }
+
+  # Force conversion to character
+  x <- as.character(x)
+
+  if (grepl("^[0-9]+$", x)) {
+    # If the string represents a single numeric value
+    return(as.numeric(x))
+  } else {
+    # Convert string representation of a list to a numeric vector
+    # Use a regular expression to split by common separators
+    return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
+  }
+}
+
+for (arg in names(args)) {
+  args[[arg]] <- convertNullString(args[[arg]])
+}
+
+# Convert only the 'psg_list' element in args
+args$psg_list <- convert_psg_list(args$psg_list)
+
 print("Argument types:")
 print(sapply(args, class))
 
@@ -66,7 +101,7 @@ print(xa)
 
 # Apply the groupCorr function to the xsAnnotate object
 print("Calling groupCorr function:")
-xa <- groupCorr(xa, cor_eic_th = args$cor_eic_th, pval = args$pval, graphMethod = args$graphMethod, calcIso = args$calcIso, calcCiS = args$calcCiS, calcCaS = args$calcCaS, cor_exp_th = args$cor_exp_th, intval = args$intval)
+xa <- groupCorr(xa, cor_eic_th = args$cor_eic_th, pval = args$pval, graphMethod = args$graphMethod, calcIso = args$calcIso, calcCiS = args$calcCiS, calcCaS = args$calcCaS, psg_list = args$psg_list, cor_exp_th = args$cor_exp_th, intval = args$intval)
 
 print("Result of groupCorr function:")
 print(xa)
diff --git a/tools/camera/groupCorr.xml b/tools/camera/groupCorr.xml
index 991a749d8..4e2c25929 100755
--- a/tools/camera/groupCorr.xml
+++ b/tools/camera/groupCorr.xml
@@ -21,6 +21,13 @@
 		calcIso $calcIso
 		calcCiS $calcCiS
 		calcCaS $calcCaS
+
+        #if $psg_list_block.psg_list_select == "FALSE":
+            psg_list NULL
+        #else
+            psg_list $psg_list
+        #end if
+        
 		cor_exp_th $cor_exp_th
 		intval $intval
 		numDigitsMZ $numDigitsMZ
@@ -51,6 +58,18 @@
                 <option value="maxf">maxf</option>
             <option value="area">area</option> -->
         </param>
+        <conditional name="psg_list_block">
+            <param name="psg_list_select" type="select" label="Use a personal psg_list">
+                <option value="TRUE">TRUE</option>
+                <option value="FALSE" selected="true">FALSE</option>
+            </param>
+            <when value="FALSE">
+                <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
+            </when>
+            <when value="TRUE">
+                <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
+            </when>
+        </conditional>
         <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)" />