feat: refactor structure of galaxy_tool

galaxy_tools/run_spac_template.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+# run_spac_template.sh - Minimal universal wrapper for SPAC templates
+# Version: 2.0 - Refactored with separated Python code
+set -euo pipefail
+
+PARAMS_JSON="${1:?Missing params.json path}"
+TEMPLATE_NAME="${2:?Missing template name}"
+
+# Log start
+echo "=== SPAC Template Execution ==="
+echo "Template: $TEMPLATE_NAME"
+echo "Parameters: $PARAMS_JSON"
+
+# Execute Python bridge and capture output
+"${SPAC_PYTHON:-python3}" tool_utils.py "$PARAMS_JSON" "$TEMPLATE_NAME" 2>&1 | tee tool_stdout.txt
+
+EXIT_CODE=${PIPESTATUS[0]}
+
+if [ $EXIT_CODE -ne 0 ]; then
+    echo "ERROR: Execution failed with exit code $EXIT_CODE"
+    exit $EXIT_CODE
+fi
+
+echo "=== Complete ==="
+exit 0

galaxy_tools/tool_config/boxplot_config.py

@@ -0,0 +1,11 @@
+"""Configuration for Boxplot tool"""
+
+TOOL_CONFIG = {
+    'outputs': {
+        'DataFrames': 'dataframe_folder',
+        'figures': 'figure_folder'
+    },
+    'list_params': ['Feature_s_to_Plot'],
+    'column_params': [],
+    'input_key': 'Upstream_Analysis'
+}

galaxy_tools/tool_config/load_csv_files_config.py

@@ -0,0 +1,25 @@
+"""Configuration for Load CSV Files tool"""
+
+def preprocess_load_csv(params):
+    """Special preprocessing for Load CSV Files"""
+    import os
+
+    # Handle CSV_Files path
+    if 'CSV_Files' in params:
+        if isinstance(params['CSV_Files'], list) and len(params['CSV_Files']) == 1:
+            params['CSV_Files'] = params['CSV_Files'][0]
+
+        # If single file, get directory
+        if isinstance(params['CSV_Files'], str) and os.path.isfile(params['CSV_Files']):
+            params['CSV_Files'] = os.path.dirname(params['CSV_Files'])
+
+    return params
+
+TOOL_CONFIG = {
+    'outputs': {
+        'DataFrames': 'dataframe_folder'
+    },
+    'list_params': ['String_Columns'],
+    'column_params': [],
+    'preprocess': preprocess_load_csv
+}

galaxy_tools/tool_config/setup_analysis_config.py

@@ -0,0 +1,11 @@
+"""Configuration for Setup Analysis tool"""
+
+TOOL_CONFIG = {
+    'outputs': {
+        'analysis': 'analysis_output.pickle'
+    },
+    'list_params': ['Features_to_Analyze'],
+    'column_params': ['X_Coordinate_Column', 'Y_Coordinate_Column', 
+                      'Features_to_Analyze', 'Annotation_s_'],
+    'input_key': 'Upstream_Dataset'
+}