Mercurial > repos > tduigou > create_assembly_picklists
changeset 8:bce1347453ee draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit ed922f834f891e6048385803c3004465551c911d-dirty
| author | tduigou |
|---|---|
| date | Thu, 07 Aug 2025 12:35:53 +0000 |
| parents | 9f35d1450906 |
| children | c3951e41e488 |
| files | create_assembly_picklists.xml |
| diffstat | 1 files changed, 31 insertions(+), 17 deletions(-) [+] |
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--- a/create_assembly_picklists.xml Thu Aug 07 12:26:04 2025 +0000 +++ b/create_assembly_picklists.xml Thu Aug 07 12:35:53 2025 +0000 @@ -323,29 +323,43 @@ </test> </tests> - <help><![CDATA[ +<help><![CDATA[ create_assembly_picklists ========================= Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo. -`Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_ + +`Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_ + +**Advanced parameters:** +------------------------ -**Advance parameter**: ---------------------- -* **Backbone Name(s)**: It can be one backbone or more than one (one name by line) -* **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. +- **Backbone Name(s):** It can be one backbone or more than one (one name per line). +- **Backbone Molar Ratio:** Between 0.0 and 1.0. This multiplies the backbone concentration with the part:backbone molar ratio. + For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, so half as much of it will be added. + **Note:** If the part quantity unit is ng, this calculation is not performed. + +**Mode:** +--------- + +This option allows you to choose how the tool runs: -**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://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html>`_) - - Assembly Plan (csv or excel): `Download... <https://osf.io/download/6894965a96fb8cc5376b0c92/>`_ - - Source Plate (excel): `Download... <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_ - ]]></help> +- **Standard**: Runs the tool as a standalone application. +- **DEMO**: Runs the tool with demo data. + +Demo data: + +- **GenBank File(s):** `Download GenBank files <https://files.osf.io/v1/resources/x2sj3/providers/osfstorage/689496483e21964670f62efc/?zip=>`_ + + **Note:** Make files as a collection list. + `How to make collection <https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html>`_ + +- **Assembly Plan (CSV or Excel):** `Download Assembly Plan <https://osf.io/download/6894965a96fb8cc5376b0c92/>`_ + +- **Source Plate (Excel):** `Download Source Plate <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_ +]]></help> + + <citations> <citation type="bibtex"> @unpublished{create_assembly_picklists