# HG changeset patch
# User goeckslab
# Date 1764194432 0
# Node ID 94cd9ac4a9b149e2e4697a597b3a51c7c415ee29
# Parent  1a9c42974a5a1edf83098bf829f7dc988772c17e
planemo upload for repository https://github.com/goeckslab/gleam.git commit 3188005878e1ad81b0ca59c9c4d4d40dd981acf7

diff -r 1a9c42974a5a -r 94cd9ac4a9b1 image_learner.xml
--- a/image_learner.xml	Fri Nov 21 17:35:00 2025 +0000
+++ b/image_learner.xml	Wed Nov 26 22:00:32 2025 +0000
@@ -4,13 +4,18 @@
         <container type="docker">quay.io/goeckslab/galaxy-ludwig-gpu:0.10.1</container>
     </requirements>
     <required_files>
+        <include path="constants.py" />
+        <include path="html_structure.py" />
+        <include path="image_learner_cli.py" />
+        <include path="image_workflow.py" />
+        <include path="ludwig_backend.py" />
+        <include path="metaformer_setup.py" />
+        <include path="plotly_plots.py" />
+        <include path="split_data.py" />
         <include path="utils.py" />
-        <include path="constants.py" />
-        <include path="image_learner_cli.py" />
-
+        <include path="MetaFormer/__init__.py" />
         <include path="MetaFormer/metaformer_models.py" />
         <include path="MetaFormer/metaformer_stacked_cnn.py" />
-        <include path="MetaFormer/__init__.py" />
     </required_files>
     <stdio>
         <exit_code range="137" level="fatal_oom" description="Out of Memory" />
@@ -67,7 +72,7 @@
     </command>
 
     <inputs>
-        <param name="input_csv" argument="input_csv" type="data" format="csv" optional="false" label="the metadata csv containing image_path column, label column and optional split column" />
+        <param name="input_csv" type="data" format="csv" optional="false" label="the metadata csv containing image_path column, label column and optional split column" />
         <param name="image_zip" type="data" format="zip" optional="false" label="Image zip" help="Image zip file containing your image data"/>
         <param name="model_name" type="select" optional="false" label="Select a model for your experiment" >
 
@@ -221,8 +226,7 @@
                 <!-- No additional parameters to show if the user selects 'No' -->
             </when>
         </conditional>
-        <param argument="image_resize"
-               name="image_resize"
+        <param name="image_resize"
                type="select"
                label="Image Resize"
                help="Select the size to resize images to. Original size keeps images as-is, while other options resize all images to the specified dimensions.">
@@ -240,8 +244,7 @@
             <option value="448x448">448x448</option>
             <option value="512x512">512x512</option>
         </param>
-        <param argument="augmentation"
-               name="augmentation"
+        <param name="augmentation"
                type="select"
                multiple="true"
                display="checkboxes"
@@ -381,8 +384,8 @@
             <param name="input_csv" value="mnist_subset.csv" ftype="csv" />
             <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
             <param name="model_name" value="randformer_s12" />
-            <param name="customize_defaults" value="true" />
-            <param name="epochs" value="5" />
+            <param name="advanced_settings|customize_defaults" value="true" />
+            <param name="advanced_settings|epochs" value="5" />
             <output name="output_report">
                 <assert_contents>
                     <has_text text="Results Summary" />
@@ -482,8 +485,8 @@
             <param name="input_csv" value="mnist_subset_binary.csv" ftype="csv" />
             <param name="image_zip" value="mnist_subset.zip" ftype="zip" />
             <param name="model_name" value="resnet18" />
-            <param name="customize_defaults" value="true" />
-            <param name="threshold" value="0.6" />
+            <param name="advanced_settings|customize_defaults" value="true" />
+            <param name="advanced_settings|threshold" value="0.6" />
             <output name="output_report">
                 <assert_contents>
                     <has_text text="Accuracy" />