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comparison create_assembly_picklists.xml @ 8:bce1347453ee draft

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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
comparison
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7:9f35d1450906 8:bce1347453ee
321 </assert_contents> 321 </assert_contents>
322 </output> 322 </output>
323 </test> 323 </test>
324 </tests> 324 </tests>
325 325
326 <help><![CDATA[ 326 <help><![CDATA[
327 create_assembly_picklists 327 create_assembly_picklists
328 ========================= 328 =========================
329 329
330 Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo. 330 Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo.
331 `Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_ 331
332 332 `Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_
333 **Advance parameter**: 333
334 --------------------- 334 **Advanced parameters:**
335 * **Backbone Name(s)**: It can be one backbone or more than one (one name by line) 335 ------------------------
336 * **Backbone Molar Ratio**: between 0.0 and 1.0 336
337 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. 337 - **Backbone Name(s):** It can be one backbone or more than one (one name per line).
338 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case. 338 - **Backbone Molar Ratio:** Between 0.0 and 1.0. This multiplies the backbone concentration with the part:backbone molar ratio.
339 339 For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, so half as much of it will be added.
340 **Mode**: 340 **Note:** If the part quantity unit is ng, this calculation is not performed.
341
342 **Mode:**
341 --------- 343 ---------
342 This option allows you to choose the mode in which the tool will be executed: 344
343 * **Standard**: Runs the tool as a standalone application. 345 This option allows you to choose how the tool runs:
344 * **DEMO**: Runs the tool as a standalone application with default parameters adapted to the demo dataset: 346
345 - 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>`_) 347 - **Standard**: Runs the tool as a standalone application.
346 - Assembly Plan (csv or excel): `Download... <https://osf.io/download/6894965a96fb8cc5376b0c92/>`_ 348 - **DEMO**: Runs the tool with demo data.
347 - Source Plate (excel): `Download... <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_ 349
348 ]]></help> 350 Demo data:
351
352 - **GenBank File(s):** `Download GenBank files <https://files.osf.io/v1/resources/x2sj3/providers/osfstorage/689496483e21964670f62efc/?zip=>`_
353
354 **Note:** Make files as a collection list.
355 `How to make collection <https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html>`_
356
357 - **Assembly Plan (CSV or Excel):** `Download Assembly Plan <https://osf.io/download/6894965a96fb8cc5376b0c92/>`_
358
359 - **Source Plate (Excel):** `Download Source Plate <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_
360 ]]></help>
361
362
349 <citations> 363 <citations>
350 <citation type="bibtex"> 364 <citation type="bibtex">
351 @unpublished{create_assembly_picklists 365 @unpublished{create_assembly_picklists
352 author = {Ramiz Khaled}, 366 author = {Ramiz Khaled},
353 title = {{create_assembly_picklists}}, 367 title = {{create_assembly_picklists}},