--- a/cloning_similation.xml	Mon May 19 14:14:18 2025 +0000
+++ b/cloning_similation.xml	Wed May 21 14:53:05 2025 +0000
@@ -16,13 +16,14 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
-        #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
-        #if $domesticated_input
-            #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input])
-            #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
-        #else
-            #set domesticated_input_paths = ""
-            #set file_name_mapping_dom = ""
+        #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
+        #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input])
+        #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
+        #if $domesticated_input_paths != '' and $genbank_file_paths == ''
+            #set genbank_file_paths = ','.join([str(f) for f in $domesticated_input])
+            #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
+            #set domesticated_input_paths = ''
+            #set file_name_mapping_dom = ''
         #end if
         mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
         cp '$assembly_csv' 'assembly_csv.csv' &&
@@ -38,13 +39,13 @@
             --outdir_gb 'outdir_gb'
             --output_simulation 'output_zip.zip'
             --enzyme '$adv.enzyme' 
-            --topology '$topology'&&
-        cp 'output_zip.zip' '$output_zip' 
+            --topology '$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)"/>
+        <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="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" value="None" optional="True"/>
+        <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">
             <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
             <option value="GibsonAssembly">Gibson_assembly</option>
@@ -305,11 +306,64 @@
                 </element>
             </output_collection>
         </test>
+        <!--test only domestication input-->
+        <test> 
+            <param name="domesticated_input">
+                <collection type="list">
+                    <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
+                    <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
+                    <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
+                    <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
+                    <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
+                    <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
+                    <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
+                    <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
+                    <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
+                    <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
+                    <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
+                    <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
+                </collection>
+            </param>
+            <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
+            <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
+            <param name="topology" value="circular"/>
+            <param name="adv|use_file_names_as_ids" value="True" />
+            <output name="output_zip" ftype='zip'>
+                <assert_contents>
+                    <has_archive_member path=".*" n="62"/>
+                    <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
+                        <has_size min="5"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output_collection name="construct_gb" type="list" count="4">
+                <element name="construct_1">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_2">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_3">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                 <element name="construct_4">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     
     <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/>`_).