updated test

RECETOX · Aug 16, 2024 · 8c1d424 · 8c1d424
1 parent b403f84
commit 8c1d424
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Showing 9 changed files with 5,223 additions and 6,557 deletions.
diff --git a/tools/ms2deepscore/ms2deepscore_config_generator.xml b/tools/ms2deepscore/ms2deepscore_config_generator.xml
@@ -58,8 +58,8 @@ settings.save_to_file("$output_file")
 
     <tests>
         <test expect_num_outputs="1">
-            <param name="base_dims" value="200,200" />
-            <param name="embedding_dim" value="100" />
+            <param name="base_dims" value="20,20" />
+            <param name="embedding_dim" value="15" />
             <param name="ionisation_mode" value="negative" />
             <param name="epochs" value="2" />
             <param name="batch_size" value="2" />

diff --git a/tools/ms2deepscore/ms2deepscore_similarity.xml b/tools/ms2deepscore/ms2deepscore_similarity.xml
@@ -72,8 +72,8 @@ scores.to_json("$similarity_scores")
     <tests>
         <test expect_num_outputs="1">
             <param name="use_scores" value="False"/>
-            <param name="references" value="RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
-            <param name="queries" value="RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
+            <param name="references" value="inp_filtered_library.msp" ftype="msp"/>
+            <param name="queries" value="inp_filtered_spectra.msp" ftype="msp"/>
             <param name="model" value="Trained_model.onnx" ftype="onnx"/>
             <param name="model_param" value="Model_Parameter_JSON.json" ftype="json"/>
             <output name="similarity_scores" value="msp_json_score_out.json" ftype="json" compare="diff" />

diff --git a/tools/ms2deepscore/test-data/Model_Parameter_JSON.json b/tools/ms2deepscore/test-data/Model_Parameter_JSON.json
@@ -1,9 +1,9 @@
 {
     "base_dims": [
-        200,
-        200
+        20,
+        20
     ],
-    "embedding_dim": 100,
+    "embedding_dim": 15,
     "ionisation_mode": "negative",
     "train_binning_layer": false,
     "train_binning_layer_group_size": 20,
@@ -16,7 +16,7 @@
     "weighting_factor": 0,
     "model_file_name": "ms2deepscore_model.pt",
     "history_plot_file_name": "history.svg",
-    "time_stamp": "2024_08_15_09_50_31",
+    "time_stamp": "2024_08_16_07_50_22",
     "min_mz": 10,
     "max_mz": 1000,
     "mz_bin_width": 0.1,

diff --git a/tools/ms2deepscore/test-data/RECETOX_Exposome_pesticides_HR_MS_20220323.msp b/tools/ms2deepscore/test-data/RECETOX_Exposome_pesticides_HR_MS_20220323.msp
diff --git a/tools/ms2deepscore/test-data/Trained_model.onnx b/tools/ms2deepscore/test-data/Trained_model.onnx