Merge pull request #193 from ntalluri/param-tuning-integration

Parameter Tuning Code Integration: update evaluation and add egfr gold standard

Author: agitter

Snakefile

@@ -384,4 +384,4 @@ rule evaluation:
 
 # Remove the output directory
 rule clean:
-    shell: f'rm -rf {out_dir}'
+    shell: f'rm -rf {out_dir}'

config/config.yaml

@@ -178,4 +178,9 @@ analysis:
         # 'euclidean', 'manhattan', 'cosine'
         metric: 'euclidean'
       evaluation:
+        # evaluation per dataset-goldstandard pair
+        # evaluation will not run unless ml include is set to true
         include: true
+        # adds evaluation per algorithm per dataset-goldstandard pair
+        # evaluation per algortihm will not run unless ml include and ml aggregate_per_algorithm are set to true
+        aggregate_per_algorithm: true