Delete outdated test files + try to fix singlefile problem

workflow4metabolomics · Oct 22, 2024 · c890131 · c890131
1 parent 67ef11c
commit c890131
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Showing 15 changed files with 89 additions and 1,268 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -10,13 +10,13 @@ args_vec <- commandArgs(trailingOnly = TRUE)
 print("Arguments retrieved from the command line:")
 print(args_vec)
 
-# Function to convert "NULL" strings to actual NULL values
-convertNullString <- function(x) {
-  if (x == "NULL") {
-    return(NULL)
-  }
-  return(x)
-}
+# # Function to convert "NULL" strings to actual NULL values
+# convertNullString <- function(x) {
+#   if (x == "NULL") {
+#     return(NULL)
+#   }
+#   return(x)
+# }
 
 args <- list(
   image           = args_vec[1], # the xsAnnotate object
@@ -26,23 +26,39 @@ args <- list(
   polarity        = args_vec[5], # Which polarity mode was used for measuring of the MS sample
   rules           = args_vec[6], # custom ruleset or NULL for default ruleset
   max_peaks       = as.numeric(args_vec[7]), # If run in parallel mode, this number defines how many peaks will be calculated in each thread
-  psg_list        = convertNullString(args_vec[8]), # Vector of pseudospectra indices; correlation analysis will only be done for those groups
+  psg_list        = args_vec[8], # Vector of pseudospectra indices; correlation analysis will only be done for those groups
   intval          = args_vec[9], # choose intensity values. Allowed values are "into", "maxo", "intb" (string)
   convertRTMinute = as.logical(args_vec[10]), # TRUE - FALSE
   numDigitsMZ     = as.numeric(args_vec[11]), # Number of digits MZ
   numDigitsRT     = as.numeric(args_vec[12]) # Number of digits RT
 )
-# Convert "NULL" to actual NULL or convert to data frame
-if (args$rules == "NULL") {
-  args$rulset <- convertNullString(args$rules) # Return NULL
+
+# Check if the 'rules' argument in 'args' is NULL
+if (is.null(args$rules)) {
+  # If 'args$rules' is NULL, set 'rulset' to NULL
+  args$rulset <- NULL 
 } else {
-  args$rulset <- read.table(args$rules, h = TRUE, sep = ",")
-  if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
-  if (ncol(args$rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
-  if (ncol(args$rulset) < 4) {
-    error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
+  # Try to read the rules file with different delimiters
+  delimiters <- c(";", "\t", ",")  # List of possible delimiters
+  success <- FALSE  # Flag to check if reading was successful
+
+  for (sep in delimiters) {
+    # Attempt to read the rules file with the current separator
+    args$rulset <- read.table(args$rules, header = TRUE, sep = sep)
+
+    # Check if the number of columns is at least 4
+    if (ncol(args$rulset) >= 4) {
+      success <- TRUE  # Mark success if the format is correct
+      break  # Exit the loop if the file was read successfully
+    }
+  }
+
+  # If reading the rules file failed for all delimiters
+  if (!success) {
+    # Display an error message if the file is not well formatted
+    error_message <- "The rules file appears to be improperly formatted. Accepted column separators are ;, tab, and ,."
     print(error_message)
-    stop(error_message)
+    stop(error_message)  # Stop execution with an error
   }
 }
 

diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -21,6 +21,9 @@ args <- list(
   numDigitsRT     = as.numeric(args_vec[7]) # Number of digits RT
 )
 
+print("Converted arguments:")
+print(args)
+
 # Check if the image file exists
 if (!file.exists(args$image)) {
   stop("The RData file does not exist: ", args$image)

diff --git a/tools/camera/findAdducts.xml b/tools/camera/findAdducts.xml
@@ -9,19 +9,39 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-		@COMMAND_RSCRIPT@/CAMERA_findAdducts.R
+		@COMMAND_RSCRIPT@CAMERA_findAdducts.R
 		'$image'
 		$ppm
 		$mzabs
 		$multiplier
 		$polarity
-		$rules
-		$max_peaks
-		$psg_list
+
+		#if $rules_select == "FALSE":
+            $rules NULL
+        #else
+            $rules
+        #end if
+
+        #if $advanced_select == "FALSE":
+            $multiplier 3
+            $max_peaks 100
+            $psg_list NULL
+        #else
+            $multiplier
+            $max_peaks
+            #if $psg_list_block == "FALSE":
+                $psg_list = NULL
+            #else
+                $psg_list
+            #end if
+        #end if
+
 		$intval
 		$convertRTMinute
 		$numDigitsMZ
 		$numDigitsRT
+        
+        @COMMAND_FILE_LOAD@
 		]]>
     </command>
     <inputs>
@@ -39,7 +59,7 @@
                 <option value="FALSE" selected="true">FALSE</option>
             </param>
             <when value="FALSE">
-                <param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />
+                <!--<param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />-->
             </when>
             <when value="TRUE">
                 <param name="rules" type="data" format="csv" label="User defined ruleset" />
@@ -58,9 +78,9 @@
                 <option value="FALSE" selected="true">FALSE</option>
             </param>
             <when value="FALSE">
-                <param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" />
+                <!--<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" />
                 <param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" optional="true" />
-                <param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />
+                <param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
             </when>
             <when value="TRUE">
                 <param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" />
@@ -72,7 +92,7 @@
                         <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" />
+                        <!--<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)." />
@@ -83,6 +103,7 @@
         <param name="convertRTMinute" type="boolean" checked="true" 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"/>
     </inputs>
     <outputs>
         <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findAdducts.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
@@ -91,15 +112,15 @@
     <tests>
         <test>
             <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
-            <param name="ppm" value="5" />
+            <!--<param name="ppm" value="5" />
             <param name="mzabs" value="0.015" />
             <param name="polarity" value="positive" />
             <param name="rules" value="NULL" />
             <param name="intval" value="into" />
             <param name="multiplier" value="3" />
             <param name="max_peaks" value="100" />
-            <param name="psg_list" value="NULL" />
-
+            <param name="psg_list" value="NULL" />-->
+            <expand macro="test_file_load_single"/>
             <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" />
             <output name="camera_findAdducts_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" />
         </test>

diff --git a/tools/camera/findIsotopes.xml b/tools/camera/findIsotopes.xml
@@ -9,7 +9,7 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-		@COMMAND_RSCRIPT@/CAMERA_findIsotopes.R
+		@COMMAND_RSCRIPT@CAMERA_findIsotopes.R
 		'$image'
 		$maxcharge
 		$maxiso
@@ -21,6 +21,8 @@
 		$convertRTMinute
 		$numDigitsMZ
 		$numDigitsRTF
+        
+        @COMMAND_FILE_LOAD@
 		]]>
     </command>
 
@@ -40,6 +42,7 @@
         <param name="convertRTMinute" type="boolean" checked="true" 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"/>
     </inputs>
     <outputs>
         <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.findIsotopes.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
@@ -48,14 +51,14 @@
     <tests>
         <test>
             <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
-            <param name="maxcharge" value="3" />
+            <!--<param name="maxcharge" value="3" />
             <param name="maxiso" value="4" />
             <param name="ppm" value="5" />
             <param name="mzabs" value="0.01" />
             <param name="intval" value="into" />
             <param name="minfrac" value="0.5" />
-            <param name="filter" value="FALSE" />
-
+            <param name="filter" value="FALSE" />-->
+            <expand macro="test_file_load_single"/>
             <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv" />
             <output name="camera_findIsotopes_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData" />
         </test>

diff --git a/tools/camera/groupCorr.xml b/tools/camera/groupCorr.xml
@@ -9,7 +9,7 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-		@COMMAND_RSCRIPT@/CAMERA_groupCorr.R
+		@COMMAND_RSCRIPT@CAMERA_groupCorr.R
 		'$image'
 		$cor_eic_th
 		$pval
@@ -22,6 +22,8 @@
 		$numDigitsMZ
 		$numDigitsRT
 		$convertRTMinute
+
+        @COMMAND_FILE_LOAD@
 		]]>
     </command>
 
@@ -48,6 +50,7 @@
         <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>
         <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.groupCorr.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
@@ -56,15 +59,15 @@
     <tests>
         <test>
             <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.RData" />
-            <param name="cor_eic_th" value="0.75" />
+            <!--<param name="cor_eic_th" value="0.75" />
             <param name="pval" value="0.05" />
             <param name="graphMethod" value="hcs" />
             <param name="calcIso" value="FALSE" />
             <param name="calcCiS" value="TRUE" />
             <param name="calcCaS" value="FALSE" />
             <param name="cor_exp_th" value="0.75" />
-            <param name="intval" value="into" />
-
+            <param name="intval" value="into" />-->
+            <expand macro="test_file_load_single"/>
             <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv" />
             <output name="camera_groupCorr_rdata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData" />
         </test>

diff --git a/tools/camera/groupFWHM.xml b/tools/camera/groupFWHM.xml
@@ -8,14 +8,16 @@
     <expand macro="requirements"/>
 
     <command detect_errors="exit_code"><![CDATA[
-		@COMMAND_RSCRIPT@/CAMERA_groupFWHM.R 
+		@COMMAND_RSCRIPT@CAMERA_groupFWHM.R 
 		'$image' 
 		$sigma 
 		$perfwhm 
 		$intval
 		$convertRTMinute
 		$numDigitsMZ
 		$numDigitsRT
+
+        @COMMAND_FILE_LOAD@
 		]]>
     </command>
 
@@ -31,6 +33,7 @@
         <param name="convertRTMinute" type="boolean" checked="true" 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"/>
     </inputs>
 
     <outputs>
@@ -41,10 +44,10 @@
     <tests>
         <test>
             <param name="image" value="xset.merged.groupChromPeaks.fillChromPeaks.RData" />
-            <param name="sigma" value="6" />
+            <!--<param name="sigma" value="6" />
             <param name="perfwhm" value="0.6" />
-            <param name="intval" value="into" />
-
+            <param name="intval" value="into" />-->
+            <expand macro="test_file_load_single"/>
             <output name="variableMetadata" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv" />
             <output name="camera_fwhm" file="xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata" />
         </test>

diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData
diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData
diff --git a/...ra/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData b/...ra/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData
diff --git a/.../xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData b/.../xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData