--- a/COBRAxy/flux_simulation_beta.xml	Thu Sep 11 09:35:19 2025 +0000
+++ b/COBRAxy/flux_simulation_beta.xml	Thu Sep 11 09:44:54 2025 +0000
@@ -46,6 +46,11 @@
         --seed $seed
         --output_type "${",".join(map(str, $output_types))}"
         --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
+        
+        #if 'FVA' in str($output_types_analysis):
+            --perc_opt $fva_params.optimality_fraction
+        #end if
+        
         --out_log $log
         ]]>
     </command>
@@ -100,6 +105,18 @@
             <option value="FVA" selected="false">FVA</option>
             <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
         </param>
+
+        <conditional name="fva_params">
+            <param name="show_fva_options" type="boolean" display="checkboxes" checked="false" label="Configure FVA parameters" help="Show additional FVA configuration options"/>
+            <when value="true">
+                <param name="optimality_fraction" argument="--fva_optimality" type="float" label="FVA Optimality (fraction):" value="0.90" min="0.0" max="1.0" 
+                    help="Fraction of optimality for FVA analysis. 1.0 means the flux must be optimal, lower values allow suboptimal solutions."/>
+            </when>
+            <when value="false">
+                <param name="optimality_fraction" argument="--fva_optimality" type="hidden" value="1.0"/>
+            </when>
+        </conditional>
+
     </inputs>
 
     <outputs>
@@ -127,7 +144,7 @@
 
 Flux analysis can be performed over the metabolic model:
    - parsimonious-FBA (optimized by Biomass)
-   - FVA
+   - FVA (with configurable optimality percentage)
    - Biomass sensitivity analysis (single reaction knock-out)
 
 Output:
@@ -139,6 +156,7 @@
 
 **TIP**: The Batches parameter helps maintain memory efficiency. For 10,000 samples, use n_samples=1,000 and n_batches=10.
 **TIP**: The Thinning parameter for OPTGP helps converge to stationary distribution.
+**TIP**: FVA optimality percentage allows you to explore suboptimal flux ranges. 100% restricts to optimal solutions, while lower values (e.g., 90%) allow broader flux ranges.
 ]]>
     </help>
     <expand macro="citations_fluxes" />