--- a/cloning_similation.xml	Wed May 21 14:53:05 2025 +0000
+++ b/cloning_similation.xml	Fri May 23 12:53:50 2025 +0000
@@ -38,33 +38,33 @@
             --outdir_simulation 'outdir_zip'
             --outdir_gb 'outdir_gb'
             --output_simulation 'output_zip.zip'
-            --enzyme '$adv.enzyme' 
+            --enzyme '$adv.enzyme'
             --topology '$topology' &&
         cp 'output_zip.zip' '$output_zip'
     ]]></command>
     <inputs>
         <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/>
-        <param name="assembly_csv" type="data" format="csv" label="assemnby csv"/>
+        <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"/>
-        <param name="assembly_plan_name" type="select" label="assembly calss" help="select the assambly class">
+        <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
             <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
             <option value="GibsonAssembly">Gibson_assembly</option>
             <option value="BASICAssembly">BASIC_assembly</option>
             <option value="BioBrickStandardAssembly">biobrick_assembly</option>
             <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
         </param>
-        <param name="topology" type="select" label="assambly topology" help="select circular or linear topology">
+        <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
             <option value="linear" selected="True">linear</option>
             <option value="circular">circular</option>
         </param>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use file names as sequence IDs?" />
-            <param name="enzyme" type="text" label="restrintion enzyme" value="auto" optional="True"/>
+            <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
+            <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
         </section>
     </inputs>   
     <outputs>
         <data format="zip" name="output_zip" label="simulation results"/>
-        <collection name="construct_gb" type="list" label="All constrauct GenBank">
+        <collection name="construct_gb" type="list" label="All Constract GenBank">
                 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
         </collection>
     </outputs>
@@ -369,11 +369,12 @@
 
 **Parameters**:
 ---------------
-* **assemnby csv**: csv file containes the construct names with their parts.
+* **Assemby csv**: csv file containes the construct names with their parts.
 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
-* **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**: 
+* **Domesticated GenBank**: Dimesticated GenBank list (Optional)
+* **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>`_