changeset 498:df90f40a156c draft

Uploaded

--- a/COBRAxy/flux_to_map.py	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/flux_to_map.py	Tue Sep 30 16:13:08 2025 +0000
@@ -400,7 +400,7 @@
             continue
 
         if isinstance(foldChange, str): foldChange = float(foldChange)
-        if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
+        if pValue > ARGS.pValue: # pValue above tresh: dashed arrow
             INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
             INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId, mindReactionDir = False)
 

--- a/COBRAxy/marea.py	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/marea.py	Tue Sep 30 16:13:08 2025 +0000
@@ -491,7 +491,7 @@
         if math.isnan(pValue) or (isinstance(foldChange, float) and math.isnan(foldChange)): continue
 
         if isinstance(foldChange, str): foldChange = float(foldChange)
-        if pValue >= ARGS.pValue: # pValue above tresh: dashed arrow
+        if pValue > ARGS.pValue: # pValue above tresh: dashed arrow
             INSIGNIFICANT_ARROW.styleReactionElements(metabMap, reactionId)
             continue
 

--- a/COBRAxy/metabolicModel2Tabular.py	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/metabolicModel2Tabular.py	Tue Sep 30 16:13:08 2025 +0000
@@ -36,7 +36,7 @@
     parser.add_argument("--model", type=str,
                         help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)")
     parser.add_argument("--input", type=str,
-                        help="Custom model file (JSON or XML)")
+                        help="Custom model file (JSON, XML, MAT, YAML)")
     parser.add_argument("--name", nargs='*', required=True,
                         help="Model name (default or custom)")
     
@@ -56,6 +56,43 @@
     return parser.parse_args(args)
 
 ################################- INPUT DATA LOADING -################################
+def detect_file_format(file_path: str) -> utils.FileFormat:
+    """
+    Detect file format by examining file content and extension.
+    Handles Galaxy .dat files by looking at content.
+    """
+    try:
+        with open(file_path, 'r') as f:
+            first_lines = ''.join([f.readline() for _ in range(5)])
+        
+        # Check for XML (SBML)
+        if '<?xml' in first_lines or '<sbml' in first_lines:
+            return utils.FileFormat.XML
+        
+        # Check for JSON
+        if first_lines.strip().startswith('{'):
+            return utils.FileFormat.JSON
+            
+        # Check for YAML
+        if any(line.strip().endswith(':') for line in first_lines.split('\n')[:3]):
+            return utils.FileFormat.YML
+            
+    except:
+        pass
+    
+    # Fall back to extension-based detection
+    if file_path.endswith('.xml') or file_path.endswith('.sbml'):
+        return utils.FileFormat.XML
+    elif file_path.endswith('.json'):
+        return utils.FileFormat.JSON
+    elif file_path.endswith('.mat'):
+        return utils.FileFormat.MAT
+    elif file_path.endswith('.yml') or file_path.endswith('.yaml'):
+        return utils.FileFormat.YML
+    
+    # Default to XML for unknown extensions
+    return utils.FileFormat.XML
+
 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model:
     """
     Loads a custom model from a file, either in JSON, XML, MAT, or YML format.
@@ -186,9 +223,9 @@
         ARGS.name = ' '.join(ARGS.name)
 
     if ARGS.input:
-        # Load a custom model from file
-        model = load_custom_model(
-            utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.input).ext)
+        # Load a custom model from file with auto-detected format
+        detected_format = detect_file_format(ARGS.input)
+        model = load_custom_model(utils.FilePath.fromStrPath(ARGS.input), detected_format)
     else:
         # Load a built-in model
         if not ARGS.model:

--- a/COBRAxy/metabolicModel2Tabular.xml	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/metabolicModel2Tabular.xml	Tue Sep 30 16:13:08 2025 +0000
@@ -70,7 +70,7 @@
 
             <!-- Custom model -->
             <when value="Custom_model">
-                <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
+                <param name="input" argument="--input" type="data" format="json,xml,sbml" label="Custom model file:" />
                 <conditional name="cond_medium">
                     <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
                         <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>

--- a/COBRAxy/tabular2MetabolicModel.py	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/tabular2MetabolicModel.py	Tue Sep 30 16:13:08 2025 +0000
@@ -41,7 +41,6 @@
     parser.add_argument("--output", type=str, required=True,
     help="Output model file path")
 
-
     parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
     help="Tool directory (passed from Galaxy as $__tool_directory__)")
 
@@ -86,8 +85,11 @@
                 logging.exception('Cannot create output directory: %s', out_dir)
 
         model = modelUtils.build_cobra_model_from_csv(ARGS.input)
+        
+        
+        logging.info('Created model with name: %s (ID: %s)', model.name, model.id)
 
-        # Save model in requested format
+        # Save model in requested format - Galaxy handles the filename
         if ARGS.format == "sbml":
             cobra.io.write_sbml_model(model, ARGS.output)
         elif ARGS.format == "json":
@@ -98,14 +100,17 @@
             cobra.io.save_yaml_model(model, ARGS.output)
         else:
             logging.error('Unknown format requested: %s', ARGS.format)
-            print(f"ERROR: Unknown format: {ARGS.format}")
+            raise ValueError(f"Unknown format: {ARGS.format}")
 
 
         logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)
+        print(f"Model created successfully in {ARGS.format.upper()} format")
 
-    except Exception:
+    except Exception as e:
         # Log full traceback to the out_log so Galaxy users/admins can see what happened
         logging.exception('Unhandled exception in fromCSVtoCOBRA')
+        print(f"ERROR: {str(e)}")
+        raise
 
 
 if __name__ == '__main__':

--- a/COBRAxy/tabular2MetabolicModel.xml	Tue Sep 30 15:32:27 2025 +0000
+++ b/COBRAxy/tabular2MetabolicModel.xml	Tue Sep 30 16:13:08 2025 +0000
@@ -19,7 +19,7 @@
         python $__tool_directory__/tabular2MetabolicModel.py
             --tool_dir $__tool_directory__
             --input $input 
-            --format $format 
+            --format $format
             --output $output
             --out_log $log
     ]]></command>
@@ -27,6 +27,7 @@
     <!-- Tool inputs -->
     <inputs>
         <param name="input" type="data" format="tabular,csv,tsv" label="Input table"/>
+        <param name="model_name" type="text" value="Converted_Model" label="Model name" help="Name for the created COBRA model"/>
         <param name="format" type="select" label="Output COBRA model format">
             <option value="sbml" selected="true">SBML (.xml)</option>
             <option value="json">JSON (.json)</option>
@@ -37,8 +38,8 @@
 
     <!-- Tool outputs -->
     <outputs>
-        <data name="log" format="txt" label="fromcsvtocobra - Log" />
-        <data name="output" format="xml" label="COBRA model">
+        <data name="log" format="txt" label="Tabular to Model Conversion - Log" />
+        <data name="output" format="xml" label="${model_name}.${format}">
             <change_format>
                 <when input="format" value="sbml" format="xml"/>
                 <when input="format" value="json" format="json"/>