From 4e69a4fea548b6fe9c94adcb7c001cb0ef018f6b Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 30 Dec 2024 04:15:22 +0000
Subject: [PATCH 1/2] Updating tools/flexynesis from version 0.2.10 to 0.2.12

---
 tools/flexynesis/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/flexynesis/macros.xml b/tools/flexynesis/macros.xml
index 864dde42af..5ea1659cf7 100644
--- a/tools/flexynesis/macros.xml
+++ b/tools/flexynesis/macros.xml
@@ -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">

From d005e0f2e7e70a8f99c051ec5e091c1c7efde08b Mon Sep 17 00:00:00 2001
From: Amirhossein Naghsh Nilchi <amirnnilchi@gmail.com>
Date: Wed, 8 Jan 2025 17:04:53 +0100
Subject: [PATCH 2/2] add XGBoost and tests

---
 tools/flexynesis/flexynesis.xml | 54 ++++++++++++++++++++++++++++-----
 tools/flexynesis/macros.xml     |  2 +-
 2 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/tools/flexynesis/flexynesis.xml b/tools/flexynesis/flexynesis.xml
index 7a388c8f04..21fbcb7da7 100644
--- a/tools/flexynesis/flexynesis.xml
+++ b/tools/flexynesis/flexynesis.xml
@@ -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">
@@ -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="">
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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,"/>
+                        <has_text_matching expression="GNN,Erlotinib,numerical,r2,"/>
+                        <has_text_matching expression="GNN,Erlotinib,numerical,pearson_corr,"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -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
diff --git a/tools/flexynesis/macros.xml b/tools/flexynesis/macros.xml
index 864dde42af..5ea1659cf7 100644
--- a/tools/flexynesis/macros.xml
+++ b/tools/flexynesis/macros.xml
@@ -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">