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comparison create_assembly_picklists.xml @ 5:bb70a954048e 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 12:16:27 +0000
parents 0b8f66f0383a
children efd0c39c6bee
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4:0b8f66f0383a 5:bb70a954048e
89 <param name="backbone_name" type="text" area="True" value='HC_Amp_ccdB' label="Backbone Name(s)" optional='true'/> 89 <param name="backbone_name" type="text" area="True" value='HC_Amp_ccdB' label="Backbone Name(s)" optional='true'/>
90 <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' /> 90 <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
91 </section> 91 </section>
92 </when> 92 </when>
93 </conditional> 93 </conditional>
94 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" /> 94 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank File(s)" />
95 <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/> 95 <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/>
96 <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/> 96 <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/>
97 </inputs> 97 </inputs>
98 <outputs> 98 <outputs>
99 <data format="zip" name="output_zip" label="picklist (zip)"/> 99 <data format="zip" name="output_zip" label="picklist (zip)"/>
334 --------------------- 334 ---------------------
335 * **Backbone Name(s)**: It can be one backbone or more than one (one name by line) 335 * **Backbone Name(s)**: It can be one backbone or more than one (one name by line)
336 * **Backbone Molar Ratio**: between 0.0 and 1.0 336 * **Backbone Molar Ratio**: between 0.0 and 1.0
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 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.
338 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case. 338 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case.
339
340 **Mode**:
341 ---------
342 This option allows you to choose the mode in which the tool will be executed:
343 * **Standard**: Runs the tool as a standalone application.
344 * **DEMO**: Runs the tool as a standalone application with default parameters adapted to the demo dataset:
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://files.osf.io/v1/resources/x2sj3/providers/osfstorage/689496483e21964670f62efc/?zip=>`_)
346 - Assembly Plan (csv or excel): `Download... <hhttps://osf.io/download/6894965a96fb8cc5376b0c92/>`_
347 - Source Plate (excel): `Download... <https://osf.io/download/6894965b7d01c1cf281b52d3/>`_
339 ]]></help> 348 ]]></help>
340 <citations> 349 <citations>
341 <citation type="bibtex"> 350 <citation type="bibtex">
342 @unpublished{create_assembly_picklists 351 @unpublished{create_assembly_picklists
343 author = {Ramiz Khaled}, 352 author = {Ramiz Khaled},