# HG changeset patch
# User bgruening
# Date 1760645823 0
# Node ID e0a67265f3ed30c7a2bd5be1bf7b5d334c8bc0ec
# Parent  9c91d13827efe82e9624c2a7fdb380a8877f56c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit bcee55468e70cd025cc5359bef5e9991e893eca9

diff -r 9c91d13827ef -r e0a67265f3ed flexynesis.xml
--- a/flexynesis.xml	Wed Jul 23 07:50:31 2025 +0000
+++ b/flexynesis.xml	Thu Oct 16 20:17:03 2025 +0000
@@ -146,6 +146,8 @@
             $use_cv
             $evaluate_baseline_performance
             --feature_importance_method $feature_importance_method
+            --safetensors
+            --threads "\${GALAXY_SLOTS:-4}"
             \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
 
         ## convert flexynesis output files to tabular format
@@ -489,11 +491,15 @@
                 <expand macro="advanced"/>
             </when>
         </conditional>
+        <param name="safetensors_out_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Save the trained model?" help="The model will be saved as Safetensors format." />
     </inputs>
     <outputs>
         <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
             <discover_datasets pattern="(?P&lt;name&gt;.+)\.tabular$" format="tabular" directory="output"/>
         </collection>
+        <data name="model" format="safetensors" from_work_dir="output/job.final_model.safetensors" label="${tool.name} on ${on_string}: trained_model">
+            <filter>safetensors_out_bool == True</filter>
+        </data>
         <collection name="plots" type="list" label="${tool.name} on ${on_string}: plots">
             <discover_datasets pattern="__name_and_ext__" directory="plots"/>
             <filter>training_type['model'] == 's_train' and (training_type['plot']['plot_embeddings_conditional']['plot_embeddings'] == 'yes' or training_type['plot']['plot_km_conditional']['plot_km'] == 'yes' or training_type['plot']['plot_cox_conditional']['plot_cox'] == 'yes' or training_type['plot']['plot_scatter_conditional']['plot_scatter'] == 'yes' or training_type['plot']['plot_concordance_conditional']['plot_concordance'] == 'yes' or training_type['plot']['plot_pr_curves_conditional']['plot_pr_curves'] == 'yes' or training_type['plot']['plot_roc_curves_conditional']['plot_roc_curves'] == 'yes' or training_type['plot']['plot_boxplot_conditional']['plot_boxplot'] == 'yes')</filter>
@@ -501,7 +507,7 @@
     </outputs>
     <tests>
         <!-- test 1: Supervised training with GEX and CNV data, DirectPred model, Erlotinib target -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="non_commercial_use" value="True"/>
             <conditional name="training_type">
                 <param name="model" value="s_train"/>
@@ -572,6 +578,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="model" ftype="safetensors">
+                <assert_contents>
+                    <has_size value="107104"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- test 2: Supervised training with GEX data, DirectPred model, Erlotinib target -->
         <test expect_num_outputs="1">
@@ -591,6 +602,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -659,6 +671,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -710,7 +723,7 @@
             </output_collection>
         </test>
         <!-- test 4: Un-supervised training with GEX and CNV data, supervised_vae model -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="non_commercial_use" value="True"/>
             <conditional name="training_type">
                 <param name="model" value="us_train"/>
@@ -751,9 +764,14 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="model" ftype="safetensors">
+                <assert_contents>
+                    <has_size value="198076"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- test 5: Cross-modality training with GEX and CNV data, CrossModalPred model -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="non_commercial_use" value="True"/>
             <conditional name="training_type">
                 <param name="model" value="cm_train"/>
@@ -806,6 +824,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <output name="model" ftype="safetensors">
+                <assert_contents>
+                    <has_size value="194476"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- test 6: Supervised training with GEX and CNV data, GNN model, Erlotinib target -->
         <test expect_num_outputs="1">
@@ -833,6 +856,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -903,6 +927,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -949,6 +974,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.stats">
                     <assert_contents>
@@ -984,6 +1010,7 @@
                     <param name="val_size" value="0.2"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -1057,6 +1084,7 @@
                     </conditional>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="results" type="list">
                 <element name="job.embeddings_test">
                     <assert_contents>
@@ -1136,6 +1164,7 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="clin_km_km_risk_subtypes">
                     <assert_contents>
@@ -1161,13 +1190,14 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.feature_importance.IntegratedGradients_cox_hazard_ratios">
                     <assert_contents>
-                        <has_image_center_of_mass center_of_mass="972,737" eps="20"/>
+                        <has_image_center_of_mass center_of_mass="972,737" eps="40"/>
                         <has_image_channels channels="3"/>
-                        <has_image_height height="1461" delta="10"/>
-                        <has_image_width width="1941" delta="10"/>
+                        <has_image_height height="1500" delta="20"/>
+                        <has_image_width width="1980" delta="20"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -1183,6 +1213,7 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.predicted_labels_scatter_Erlotinib">
                     <assert_contents>
@@ -1205,6 +1236,7 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.predicted_labels_concordance_Erlotinib">
                     <assert_contents>
@@ -1227,6 +1259,7 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.predicted_labels_pr_curves_class">
                     <assert_contents>
@@ -1249,6 +1282,7 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.predicted_labels_roc_curves_class">
                     <assert_contents>
@@ -1271,6 +1305,7 @@
                 </conditional>
             </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.predicted_labels_box_plot_class_buz">
                     <assert_contents>
@@ -1308,13 +1343,14 @@
                     </conditional>
                 </section>
             </expand>
+            <param name="safetensors_out_bool" value="False"/>
             <output_collection name="plots" type="list">
                 <element name="job.feature_importance.IntegratedGradients_cox_hazard_ratios">
                     <assert_contents>
-                        <has_image_center_of_mass center_of_mass="972,737" eps="20"/>
+                        <has_image_center_of_mass center_of_mass="972,737" eps="40"/>
                         <has_image_channels channels="3"/>
-                        <has_image_height height="1461" delta="10"/>
-                        <has_image_width width="1941" delta="10"/>
+                        <has_image_height height="1500" delta="20"/>
+                        <has_image_width width="1980" delta="20"/>
                     </assert_contents>
                 </element>
             </output_collection>
@@ -1342,6 +1378,7 @@
                     <param name="hpo_iter" value="1"/>
                 </section>
             </conditional>
+            <param name="safetensors_out_bool" value="False"/>
             <assert_stdout>
                 <has_text_matching expression="Target variables: Erlotinib,Crizotinib"/>
             </assert_stdout>
diff -r 9c91d13827ef -r e0a67265f3ed flexynesis_plot.py
--- a/flexynesis_plot.py	Wed Jul 23 07:50:31 2025 +0000
+++ b/flexynesis_plot.py	Thu Oct 16 20:17:03 2025 +0000
@@ -11,7 +11,7 @@
 import numpy as np
 import pandas as pd
 import seaborn as sns
-from flexynesis import (
+from flexynesis.utils import (
     build_cox_model,
     plot_dim_reduced,
     plot_hazard_ratios,
diff -r 9c91d13827ef -r e0a67265f3ed macros.xml
--- a/macros.xml	Wed Jul 23 07:50:31 2025 +0000
+++ b/macros.xml	Thu Oct 16 20:17:03 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.20</token>
-    <token name="@VERSION_SUFFIX@">3</token>
-    <token name="@PROFILE@">24.1</token>
+    <token name="@TOOL_VERSION@">1.1.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">flexynesis</requirement>