--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cloning_similation.xml	Fri May 16 09:39:03 2025 +0000
@@ -0,0 +1,251 @@
+<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@">0</token>
+        <token name="@TOOL_VERSION@">0.1.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="0.1.11">flametree</requirement>
+        <requirement type="package" version="1.85"> biopython </requirement>
+        <requirement type="package" version="0.1.10">proglog</requirement>
+        <requirement type="package" version="2.2.3">pandas</requirement>
+        <requirement type="package" version="2.0.12">dnacauldron</requirement>
+        <requirement type="package" version="0.3.9">pdf-reports</requirement>
+        <requirement type="package" version="0.1.8">sequenticon</requirement>
+        <requirement type="package" version="3.1.5">dna_features_viewer</requirement>
+    </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 $domesticated_input])
+        #else
+            #set domesticated_input_paths = ""
+            #set file_name_mapping_dom = ""
+        #end if
+        mkdir 'outdir_zip' &&
+        python '$__tool_directory__/cloning_simulation.py'
+            --parts_files '$genbank_file_paths'
+            --domesticated_seq '$domesticated_input_paths'
+            --assembly_csv '$assembly_csv'
+            --assembly_plan_name '$assembly_plan_name'
+            --file_name_mapping '$file_name_mapping'
+            --file_name_mapping_dom '$file_name_mapping_dom'
+            --use_file_names_as_id '$adv.use_file_names_as_ids'
+            --outdir_simulation 'outdir_zip'
+            --output_simulation 'output_zip.zip'
+            --enzyme '$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 File(s)"/>
+        <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="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">
+            <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"/>
+        </section>
+    </inputs>   
+    <outputs>
+        <data format="zip" name="output_zip" label="simulation results"/>
+    </outputs>
+    <tests>
+        <!--test type2s_assembly class-->
+        <test> 
+            <param name="genbank_files">
+                <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>
+        </test>
+        <!--test gibson_assembly class-->
+        <test> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" />
+                </collection>
+            </param>
+            <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
+            <param name='assembly_plan_name' value='GibsonAssembly' />
+            <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="78"/>
+                    <has_archive_member path="assambly_simulation/Report.pdf">
+                        <has_size min="5"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <!--test lcr_assembly class-->
+        <test> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
+                    <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
+                </collection>
+            </param>
+            <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
+            <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
+            <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="68"/>
+                    <has_archive_member path="assambly_simulation/Report.pdf">
+                        <has_size min="5"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <!--test BASIC_assembly class-->
+        <test> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="GFP" value="BASIC_assembly_dataset/GFP.gb" />
+                    <element name="p15A_kan" value="BASIC_assembly_dataset/p15A_kan.gb" />
+                    <element name="promoter" value="BASIC_assembly_dataset/promoter.gb" />
+                    <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" />
+                    <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" />
+                </collection>
+            </param>
+            <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
+            <param name='assembly_plan_name' value='BASICAssembly' />
+            <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="47"/>
+                    <has_archive_member path="assambly_simulation/Report.pdf">
+                        <has_size min="5"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <!--test biobrick_assembly class-->
+        <test> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="BBa_E0040_GFP" value="BioBrick_assembly_dataset/BBa_E0040_GFP.gb" />
+                    <element name="BBa_J23119_prom" value="BioBrick_assembly_dataset/BBa_J23119_prom.gb" />
+                    <element name="BBa_J23119_prom_flawed" value="BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb" />
+                    <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" />
+                    <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" />
+                </collection>
+            </param>
+            <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
+            <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
+            <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="47"/>
+                    <has_archive_member path="assambly_simulation/Report.pdf">
+                        <has_size min="5"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <!--test type2s_assembly with domesticated files-->
+        <test> 
+            <param name="genbank_files">
+                <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" />
+                </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="domesticated_input">
+                <collection type="list">
+                    <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="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>
+        </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/>`_).
+
+**Parameters**:
+---------------
+* **assemnby 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**: 
+    - "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>`_
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{cloning_simulation
+                author = {Ramiz Khaled},
+                title = {{cloning_simulation}},
+                url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
+            }
+        </citation>
+    </citations>
+</tool>