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Updating tools/flexynesis from version 0.2.10 to 0.2.12 #1563

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Jan 8, 2025
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Updating tools/flexynesis from version 0.2.10 to 0.2.12 #1563

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4e69a4f
Updating tools/flexynesis from version 0.2.10 to 0.2.12
Dec 30, 2024
d005e0f
add XGBoost and tests
nilchia Jan 8, 2025
f99251d
Merge pull request #4 from nilchia/flexy_0.2.12
bgruening Jan 8, 2025
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54 changes: 47 additions & 7 deletions tools/flexynesis/flexynesis.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,7 @@
<option value="RandomForest">RandomForest</option>
<option value="SVM">SVM</option>
<option value="RandomSurvivalForest">RandomSurvivalForest</option>
<option value="XGBoost">XGBoost</option>
</param>
<when value="DirectPred"/>
<when value="GNN">
Expand All @@ -133,6 +134,7 @@
<when value="RandomForest"/>
<when value="SVM"/>
<when value="RandomSurvivalForest"/>
<when value="XGBoost"/>
</conditional>
<param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
<sanitizer invalid_char="">
Expand Down Expand Up @@ -201,7 +203,9 @@
</repeat>
<conditional name="training_type">
<param name="model" value="s_train"/>
<param name="model_class" value="DirectPred"/>
<conditional name="model_class">
<param name="model_class" value="DirectPred"/>
</conditional>
<param name="target_variables" value="Erlotinib"/>
</conditional>
<param name="hpo_iter" value="1"/>
Expand Down Expand Up @@ -256,7 +260,9 @@
<param name="assay_main" value="bar"/>
<conditional name="training_type">
<param name="model" value="s_train"/>
<param name="model_class" value="DirectPred"/>
<conditional name="model_class">
<param name="model_class" value="DirectPred"/>
</conditional>
<param name="target_variables" value="Erlotinib"/>
</conditional>
<param name="hpo_iter" value="1"/>
Expand Down Expand Up @@ -311,7 +317,9 @@
</repeat>
<conditional name="training_type">
<param name="model" value="s_train"/>
<param name="model_class" value="DirectPred"/>
<conditional name="model_class">
<param name="model_class" value="DirectPred"/>
</conditional>
<param name="target_variables" value="Irinotecan"/>
</conditional>
<param name="hpo_iter" value="1"/>
Expand Down Expand Up @@ -463,7 +471,9 @@
</repeat>
<conditional name="training_type">
<param name="model" value="s_train"/>
<param name="model_class" value="GNN"/>
<conditional name="model_class">
<param name="model_class" value="GNN"/>
</conditional>
<param name="gnn_conv_type" value="GC"/>
<param name="string_organism" value="9606"/>
<param name="string_node_name" value="gene_name"/>
Expand Down Expand Up @@ -505,9 +515,9 @@
</element>
<element name="job.stats">
<assert_contents>
<has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
<has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
<has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
<has_text_matching expression="GNN,Erlotinib,numerical,mse,"/>
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Why did it change from DirectPred to GNN?

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This one is correct actually. In the previous test <param name="model_class" value="GNN"/> was not enclosed within the <conditional name="model_class"> and </conditional>, and instead of GNN, the default model (DirectPred) was called.

The other tests are correct.

<has_text_matching expression="GNN,Erlotinib,numerical,r2,"/>
<has_text_matching expression="GNN,Erlotinib,numerical,pearson_corr,"/>
</assert_contents>
</element>
</output_collection>
Expand Down Expand Up @@ -552,6 +562,36 @@
</element>
</output_collection>
</test>
<test>
<param name="non_commercial_use" value="True"/>
<param name="train_clin" value="train/clin" ftype="csv"/>
<param name="test_clin" value="test/clin" ftype="csv"/>
<param name="train_omics_main" value="train/gex" ftype="csv"/>
<param name="test_omics_main" value="test/gex" ftype="csv"/>
<param name="assay_main" value="bar"/>
<repeat name="omics">
<param name="train_omics" value="train/cnv" ftype="csv"/>
<param name="test_omics" value="test/cnv" ftype="csv"/>
<param name="assay" value="foo"/>
</repeat>
<conditional name="training_type">
<param name="model" value="s_train"/>
<conditional name="model_class">
<param name="model_class" value="XGBoost"/>
</conditional>
<param name="target_variables" value="Erlotinib"/>
</conditional>
<param name="hpo_iter" value="1"/>
<output_collection name="results" type="list">
<element name="job.stats">
<assert_contents>
<has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,mse,"/>
<has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,r2,"/>
<has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,pearson_corr,"/>
</assert_contents>
</element>
</output_collection>
</test>
</tests>
<help>
.. class:: warningmark
Expand Down
2 changes: 1 addition & 1 deletion tools/flexynesis/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">0.2.10</token>
<token name="@TOOL_VERSION@">0.2.12</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">24.1</token>
<xml name="requirements">
Expand Down
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