Mercurial > repos > bimib > cobraxy

changeset 436:13e99c8e4e81 draft

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Uploaded
author francesco_lapi
date Wed, 10 Sep 2025 15:35:55 +0000
parents ee2b1adb02bf
children 44f91eba4776
files COBRAxy/flux_simulation_beta.xml
diffstat 1 files changed, 7 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/flux_simulation_beta.xml	Wed Sep 10 15:33:00 2025 +0000
+++ b/COBRAxy/flux_simulation_beta.xml	Wed Sep 10 15:35:55 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="fluxSimulationBeta" name="Flux Simulation - BETA" version="2.0.0">
+<tool id="fluxSimulation - Beta" name="Flux Simulation - BETA" version="2.0.0">
     
     <macros>
         <import>marea_macros.xml</import>
@@ -44,11 +44,8 @@
         --n_batches $n_batches
         --n_samples $n_samples
         --seed $seed
-
-        --perc_opt $output_types_analysis_cond.fva_fraction
-
         --output_type "${",".join(map(str, $output_types))}"
-        --output_type_analysis "${",".join(map(str, $output_types_analysis_cond.output_types_analysis))}"
+        --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
         --out_log $log
         ]]>
     </command>
@@ -98,18 +95,11 @@
             <option value="fluxes" selected="false">All fluxes</option>
         </param>
 
-        <conditional name="output_types_analysis_cond">
-            <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis">
-                <option value="pFBA" selected="false">pFBA</option>
-                <option value="FVA" selected="false">FVA</option>
-                <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
-            </param>
-
-            <when value="FVA">
-                <param name="fva_fraction" argument="--fva_fraction" type="float" label="FVA fraction of optimality (0-1):" value="0.9" min="0.0" max="1.0" help="Fraction of the optimal objective value to consider for FVA. 0.9 = 90%"/>
-            </when>
-
-        </conditional>
+        <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis">
+            <option value="pFBA" selected="false">pFBA</option>
+            <option value="FVA" selected="false">FVA</option>
+            <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
+        </param>
     </inputs>
 
     <outputs>