--- a/COBRAxy/flux_simulation_beta.xml	Mon Sep 22 13:54:43 2025 +0000
+++ b/COBRAxy/flux_simulation_beta.xml	Mon Sep 22 14:25:05 2025 +0000
@@ -36,7 +36,7 @@
             --name $names
         #end if
         
-        #if $sampling_params.enable_sampling == 'True':
+        #if $sampling_params.enable_sampling == 'true':
             --thinning 0
             #if $sampling_params.algorithm_param.algorithm == 'OPTGP':
                 --thinning $sampling_params.algorithm_param.thinning
@@ -73,9 +73,9 @@
             </param>
 
             <when value="True">
-                <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular"
-                    label="Model tabular file:"
-                    help="Upload a CSV/TSV file that contains the model reaction rules. Recommended columns: ReactionID, Reaction (formula), Rule (GPR). Optional columns: name, lower_bound, upper_bound, InMedium. If bounds are present here they may be overridden by separate bound files." />
+                <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular" multiple="false"
+                    label="Model file:"
+                    help="Upload a CSV/TSV file containing information generated by the Model Initialization tool." />
 
                 <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular,csv,tsv"
                     label="Bound file(s):"
@@ -90,12 +90,9 @@
         </conditional>
 
         <conditional name="sampling_params">
-            <param name="enable_sampling" type="select" label="Enable sampling:" help="Choose whether to perform flux sampling in addition to optimization analyses.">
-                <option value="False" selected="true">No sampling (optimization only)</option>
-                <option value="True">Enable sampling</option>
-            </param>
+            <param name="enable_sampling" type="boolean" display="checkboxes" checked="false" label="Enable sampling" help="Check this box to perform flux sampling in addition to optimization analyses"/>
             
-            <when value="True">
+            <when value="true">
                 <conditional name="algorithm_param">
                     <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
                         <option value="CBS" selected="true">CBS</option>
@@ -109,7 +106,7 @@
                 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000" help="Number of samples to generate."/>
                 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="This is useful for computational performances."/>
 
-                <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling">
+                <param type="select" argument="--output_types" multiple="true" name="output_types" label="Choose outputs from sampling">
                     <option value="mean" selected="true">Mean</option>
                     <option value="median" selected="false">Median</option>
                     <option value="quantiles" selected="false">Quantiles</option>
@@ -118,9 +115,12 @@
 
                 <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" help="Random seed for sampling algorithms."/>
             </when>
+            <when value="false">
+                <!-- Hidden parameters with default values when sampling is disabled -->
+            </when>
         </conditional>
 
-        <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from optimization">
+        <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Choose outputs from optimization">
             <option value="pFBA" selected="false">pFBA</option>
             <option value="FVA" selected="true">FVA</option>
             <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>