--- a/cloning_similation.xml	Wed Jul 23 09:46:59 2025 +0000
+++ b/cloning_similation.xml	Tue Jan 06 11:34:13 2026 +0000
@@ -1,7 +1,7 @@
 <tool id="cloning_simulation" name="Cloning Simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>A cloning simulator for synthetic biology</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
         <token name="@TOOL_VERSION@">0.2.0</token>
     </macros>
     <requirements>
@@ -34,7 +34,7 @@
             --file_name_mapping '$file_name_mapping'
             --file_name_mapping_dom '$file_name_mapping_dom'
             --use_json_paramers '$json_use.use_json_paramers'
-            #if not $json_use.use_json_paramers:
+            #if $json_use.use_json_paramers=='false':
                 --enzyme '$json_use.enzyme'
                 --topology '$json_use.topology'
                 --assembly_plan_name '$json_use.assembly_plan_name'
@@ -52,7 +52,10 @@
         <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/>
         <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/>
         <conditional name="json_use">
-            <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
+            <param name="use_json_paramers" type="select" label="Use parameters from JSON" help="extract parameters from json file">
+                <option value="true">Get Parameters From JSON</option>
+                <option value="false" selected="true">Set Parameters Manually</option>
+            </param>
             <when value="false">
                 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
                     <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
@@ -99,7 +102,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
                 <param name="topology" value="circular"/>
@@ -144,7 +147,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='GibsonAssembly' />
                 <param name="topology" value="circular"/>
@@ -185,7 +188,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
                 <param name="topology" value="circular"/>
@@ -214,7 +217,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='BASICAssembly' />
                 <param name="topology" value="circular"/>
@@ -243,7 +246,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
                 <param name="topology" value="circular"/>
@@ -289,7 +292,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />   
                 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
                 <param name="topology" value="circular"/>
@@ -354,7 +357,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name='use_json_paramers' value='false' />
                 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
                 <param name="topology" value="circular"/>
@@ -410,7 +413,7 @@
                 </collection>
             </param>
             <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
-            <conditional nam="json_use">
+            <conditional name="json_use">
                 <param name="use_json_paramers" value='true'/>
                 <param name="json_conf" value="test-JSON.json" />
             </conditional>
@@ -450,12 +453,12 @@
     
     <help><![CDATA[
 Cloning_Simulation
-    ====================
+====================
 
 The Cloning Simulation tool is based on the DnaCauldron package developed by the EGF Biofoundry. It enables rapid and accurate assembly simulation of DNA parts for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaCauldron/>`_).
 
 **Parameters**:
----------------
+----------------
 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
@@ -463,11 +466,11 @@
 * **Topology**: Can be "circular", "linear".
 * **Enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_ 
 * **Assembly Class**: 
-    - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
-    - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
-    - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
-    - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
-    - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_
+    - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `Golden Gate dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
+    - "gibson_assembly": GibsonAssembly `Gibson dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
+    - "BASIC_assembly": BASICAssembly `BASIC dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
+    - "biobrick_assembly": BioBrickStandardAssembly, `biobrick dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
+    - "lcr_assembly": LigaseCyclingReactionAssembly `lcr dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_
     ]]></help>
     <citations>
         <citation type="bibtex">