--- a/create_assembly_picklists.xml	Wed Aug 06 14:42:41 2025 +0000
+++ b/create_assembly_picklists.xml	Thu Aug 07 11:55:14 2025 +0000
@@ -38,36 +38,62 @@
             --parts_files '$renamed_paths'
             --picklist '$picklist'
             --source_plate 'source_plate.xlsx'
-            --backbone_name '$adv.backbone_name'
-            --part_backbone_ratio '$adv.part_backbone_ratio'
-            --quantity_unit '$quantity_unit'
-            --part_quantity '$part_quantity'
-            --buffer_volume '$buffer_volume'
-            --total_volume '$total_volume'
-            --dispenser '$dispenser'
+            --backbone_name '$setting.adv.backbone_name'
+            --part_backbone_ratio '$setting.adv.part_backbone_ratio'
+            --quantity_unit '$setting.quantity_unit'
+            --part_quantity '$setting.part_quantity'
+            --buffer_volume '$setting.buffer_volume'
+            --total_volume '$setting.total_volume'
+            --dispenser '$setting.dispenser'
             --result_zip 'picklist.zip' &&
         cp 'picklist.zip' '$output_zip' 
     ]]></command>
     <inputs>
+        <conditional name='setting'>
+            <param name="mode" type="select" label="Mode">
+                <option value="std" selected="true">Standard</option>
+                <option value="demo">DEMO</option>
+            </param>
+            <when value="std">
+                <param name="quantity_unit" type="select" label="Part quantity unit">
+                    <option value="fmol" selected="true">femto-mole</option>
+                    <option value="nM">nano-molar</option>
+                    <option value="ng">nano-gram</option>
+                </param>
+                <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
+                <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
+                <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
+                <param name="dispenser" type="select" label="Dispenser Machine">
+                    <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
+                    <option value="tecan_evo">Tecab EVO</option>
+                </param>
+                <section name="adv" title="advance" expanded="false">
+                    <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" optional='true'/>
+                    <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
+                </section>
+            </when>
+            <when value="demo">
+                <param name="quantity_unit" type="select" label="Part quantity unit">
+                    <option value="fmol" selected="true">femto-mole</option>
+                    <option value="nM">nano-molar</option>
+                    <option value="ng">nano-gram</option>
+                </param>
+                <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
+                <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
+                <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
+                <param name="dispenser" type="select" label="Dispenser Machine">
+                    <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
+                    <option value="tecan_evo">Tecab EVO</option>
+                </param>
+                <section name="adv" title="advance" expanded="false">
+                    <param name="backbone_name" type="text" area="True" value='HC_Amp_ccdB' label="Backbone Name(s)" optional='true'/>
+                    <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
+                </section>
+            </when>
+        </conditional>
         <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" />
         <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/>
         <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/>
-        <param name="quantity_unit" type="select" label="Part quantity unit">
-            <option value="fmol" selected="true">femto-mole</option>
-            <option value="nM">nano-molar</option>
-            <option value="ng">nano-gram</option>
-        </param>
-        <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
-        <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
-        <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
-        <param name="dispenser" type="select" label="Dispenser Machine">
-            <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
-            <option value="tecan_evo">Tecab EVO</option>
-        </param>
-        <section name="adv" title="advance" expanded="false">
-            <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" optional='true'/>
-            <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
-        </section>
     </inputs>   
     <outputs>
         <data format="zip" name="output_zip" label="picklist (zip)"/>
@@ -173,11 +199,122 @@
             </param>
             <param name="picklist" value="example_picklist.xls" />
             <param name="source_plate" value="example_echo_plate.xlsx"/>
-            <param name="quantity_unit" value="fmol" />
-            <param name="part_quantity" value="1.3" />
-            <param name="buffer_volume" value="0.3" />
-            <param name="total_volume" value="1.0" />
-            <param name="dispenser" value="labcyte_echo" />
+            <conditional name='setting'>
+                <param name="mode" value="std" />
+                <param name="quantity_unit" value="fmol" />
+                <param name="part_quantity" value="1.3" />
+                <param name="buffer_volume" value="0.3" />
+                <param name="total_volume" value="1.0" />
+                <param name="dispenser" value="labcyte_echo" />
+            </conditional>
+            <output name="output_zip" ftype='zip'>
+                <assert_contents>
+                    <has_archive_member path=".*" n="5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!--test demo-->
+        <test> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="HC_Amp_ccdB" value="emma_parts/HC_Amp_ccdB.gb" />
+                    <element name="conn a-c" value="emma_parts/conn a-c.gb" />
+                    <element name="conn b-e" value="emma_parts/conn b-e.gb" />
+                    <element name="conn b-l" value="emma_parts/conn b-l.gb" />
+                    <element name="conn d-e" value="emma_parts/conn d-e.gb" />
+                    <element name="conn d-f" value="emma_parts/conn d-f.gb" />
+                    <element name="conn h-ha" value="emma_parts/conn h-ha.gb" />
+                    <element name="conn h-j" value="emma_parts/conn h-j.gb" />
+                    <element name="conn h-k" value="emma_parts/conn h-k.gb" />
+                    <element name="conn j-k" value="emma_parts/conn j-k.gb" />
+                    <element name="conn l-n" value="emma_parts/conn l-n.gb" />
+                    <element name="conn l-r" value="emma_parts/conn l-r.gb" />
+                    <element name="conn l-w" value="emma_parts/conn l-w.gb" />
+                    <element name="conn l-y" value="emma_parts/conn l-y.gb" />
+                    <element name="conn q-r" value="emma_parts/conn q-r.gb" />
+                    <element name="conn r-w" value="emma_parts/conn r-w.gb" />
+                    <element name="conn t-v" value="emma_parts/conn t-v.gb" />
+                    <element name="conn w-x" value="emma_parts/conn w-x.gb" />
+                    <element name="conn w-y" value="emma_parts/conn w-y.gb" />
+                    <element name="conn w-z" value="emma_parts/conn w-z.gb" />
+                    <element name="conn y-z" value="emma_parts/conn y-z.gb" />
+                    <element name="p10_tet-aptazyme" value="emma_parts/p10_tet-aptazyme.gb" />
+                    <element name="p11_sv40polya" value="emma_parts/p11_sv40polya.gb" />
+                    <element name="p14_cmvp" value="emma_parts/p14_cmvp.gb" />
+                    <element name="p14_sv40p" value="emma_parts/p14_sv40p.gb" />
+                    <element name="p15_puror" value="emma_parts/p15_puror.gb" />
+                    <element name="p16_bghpolya" value="emma_parts/p16_bghpolya.gb" />
+                    <element name="p18_cmvp" value="emma_parts/p18_cmvp.gb" />
+                    <element name="p18_ef1ap" value="emma_parts/p18_ef1ap.gb" />
+                    <element name="p19_mneogreen" value="emma_parts/p19_mneogreen.gb" />
+                    <element name="p19_mruby2" value="emma_parts/p19_mruby2.gb" />
+                    <element name="p19_mtagbfp2" value="emma_parts/p19_mtagbfp2.gb" />
+                    <element name="p19_tet-on-3g" value="emma_parts/p19_tet-on-3g.gb" />
+                    <element name="p1_5'-itr-pb" value="emma_parts/p1_5'-itr-pb.gb" />
+                    <element name="p1_5'ha-haavs1" value="emma_parts/p1_5'ha-haavs1.gb" />
+                    <element name="p20_ct-minute-nes" value="emma_parts/p20_ct-minute-nes.gb" />
+                    <element name="p20_ct-nes" value="emma_parts/p20_ct-nes.gb" />
+                    <element name="p20_linker3" value="emma_parts/p20_linker3.gb" />
+                    <element name="p20_p2a" value="emma_parts/p20_p2a.gb" />
+                    <element name="p21_dmra" value="emma_parts/p21_dmra.gb" />
+                    <element name="p21_mkate2" value="emma_parts/p21_mkate2.gb" />
+                    <element name="p21_mneogreen" value="emma_parts/p21_mneogreen.gb" />
+                    <element name="p21_mruby2" value="emma_parts/p21_mruby2.gb" />
+                    <element name="p21_mtagbfp2" value="emma_parts/p21_mtagbfp2.gb" />
+                    <element name="p21_puror" value="emma_parts/p21_puror.gb" />
+                    <element name="p22_pgkpolya" value="emma_parts/p22_pgkpolya.gb" />
+                    <element name="p23_insulatorfb" value="emma_parts/p23_insulatorfb.gb" />
+                    <element name="p24_3'ha_haavs1" value="emma_parts/p24_3'ha_haavs1.gb" />
+                    <element name="p24_3'pb" value="emma_parts/p24_3'pb.gb" />
+                    <element name="p25_sv40-ori" value="emma_parts/p25_sv40-ori.gb" />
+                    <element name="p2_insulatorfb" value="emma_parts/p2_insulatorfb.gb" />
+                    <element name="p3_cagp" value="emma_parts/p3_cagp.gb" />
+                    <element name="p3_cmvp_tet" value="emma_parts/p3_cmvp_tet.gb" />
+                    <element name="p3_ef1ap" value="emma_parts/p3_ef1ap.gb" />
+                    <element name="p3_tre3gp" value="emma_parts/p3_tre3gp.gb" />
+                    <element name="p4_kt-l7ae -weiss" value="emma_parts/p4_kt-l7ae -weiss.gb" />
+                    <element name="p4_lac-o" value="emma_parts/p4_lac-o.gb" />
+                    <element name="p5_attb-bxb1" value="emma_parts/p5_attb-bxb1.gb" />
+                    <element name="p5_attp-bxb1" value="emma_parts/p5_attp-bxb1.gb" />
+                    <element name="p5_k1-k1" value="emma_parts/p5_k1-k1.gb" />
+                    <element name="p5_kt-weiss" value="emma_parts/p5_kt-weiss.gb" />
+                    <element name="p6_atg_boxc" value="emma_parts/p6_atg_boxc.gb" />
+                    <element name="p6_kozak-atg" value="emma_parts/p6_kozak-atg.gb" />
+                    <element name="p6_nt-igkl sequence" value="emma_parts/p6_nt-igkl sequence.gb" />
+                    <element name="p6_nt-mls" value="emma_parts/p6_nt-mls.gb" />
+                    <element name="p6_nt-myristoylation signal" value="emma_parts/p6_nt-myristoylation signal.gb" />
+                    <element name="p6_nt-palm sequence" value="emma_parts/p6_nt-palm sequence.gb" />
+                    <element name="p6_nt-sv40_nls" value="emma_parts/p6_nt-sv40_nls.gb" />
+                    <element name="p7_bxb1" value="emma_parts/p7_bxb1.gb" />
+                    <element name="p7_l7ae-weiss" value="emma_parts/p7_l7ae-weiss.gb" />
+                    <element name="p7_l7ae" value="emma_parts/p7_l7ae.gb" />
+                    <element name="p7_laci" value="emma_parts/p7_laci.gb" />
+                    <element name="p7_mcherry" value="emma_parts/p7_mcherry.gb" />
+                    <element name="p7_mkate2" value="emma_parts/p7_mkate2.gb" />
+                    <element name="p7_mneogreen" value="emma_parts/p7_mneogreen.gb" />
+                    <element name="p7_mruby2" value="emma_parts/p7_mruby2.gb" />
+                    <element name="p7_mtagbfp2" value="emma_parts/p7_mtagbfp2.gb" />
+                    <element name="p8_linker1" value="emma_parts/p8_linker1.gb" />
+                    <element name="p8_linker2" value="emma_parts/p8_linker2.gb" />
+                    <element name="p8_p2a" value="emma_parts/p8_p2a.gb" />
+                    <element name="p8a_ct-kdel" value="emma_parts/p8a_ct-kdel.gb" />
+                    <element name="p8b_ires2" value="emma_parts/p8b_ires2.gb" />
+                    <element name="p9_a-tubulin" value="emma_parts/p9_a-tubulin.gb" />
+                    <element name="p9_bsdr" value="emma_parts/p9_bsdr.gb" />
+                    <element name="p9_dmrc" value="emma_parts/p9_dmrc.gb" />
+                    <element name="p9_firefly luciferase" value="emma_parts/p9_firefly luciferase.gb" />
+                    <element name="p9_mneogreen" value="emma_parts/p9_mneogreen.gb" />
+                    <element name="p9_mruby2" value="emma_parts/p9_mruby2.gb" />
+                    <element name="p9_mtagbfp2" value="emma_parts/p9_mtagbfp2.gb" />
+                    <element name="p9_neor" value="emma_parts/p9_neor.gb" />
+                    <element name="p9_puror" value="emma_parts/p9_puror.gb" />
+                </collection>
+            </param>
+            <param name="picklist" value="example_picklist.xls" />
+            <param name="source_plate" value="example_echo_plate.xlsx"/>
+            <conditional name='setting'>
+                <param name="mode" value="demo" />
+            </conditional>
             <output name="output_zip" ftype='zip'>
                 <assert_contents>
                     <has_archive_member path=".*" n="5"/>