diff create_assembly_picklists.xml @ 5:bb70a954048e draft

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit ed922f834f891e6048385803c3004465551c911d-dirty

--- a/create_assembly_picklists.xml	Thu Aug 07 11:55:14 2025 +0000
+++ b/create_assembly_picklists.xml	Thu Aug 07 12:16:27 2025 +0000
@@ -91,7 +91,7 @@
                 </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="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank 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)"/>
     </inputs>   
@@ -336,6 +336,15 @@
 * **Backbone Molar Ratio**: between 0.0 and 1.0
 This section is to multiplie the backbone concentration with the part:backbone molar ratio. This tricks the calculator into making a picklist with the desired ratio. For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, therefore half as much of it will be added to the well.
 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case.
+
+**Mode**:
+---------
+This option allows you to choose the mode in which the tool will be executed:
+* **Standard**: Runs the tool as a standalone application.
+* **DEMO**: Runs the tool as a standalone application with default parameters adapted to the demo dataset:
+    - GenBank File(s): `Download... <https://files.osf.io/v1/resources/x2sj3/providers/osfstorage/689496483e21964670f62efc/?zip=>`_ NOTE: make files as collection list (`How to make collection <https://files.osf.io/v1/resources/x2sj3/providers/osfstorage/689496483e21964670f62efc/?zip=>`_)
+    - Assembly Plan (csv or excel): `Download... <hhttps://osf.io/download/6894965a96fb8cc5376b0c92/>`_ 
+    - Source Plate (excel): `Download... <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_ 
     ]]></help>
     <citations>
         <citation type="bibtex">