Mercurial > repos > tduigou > create_assembly_picklists

comparison create_assembly_picklists.xml @ 1:196e13c09881 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
author tduigou
date Wed, 06 Aug 2025 14:38:40 +0000
parents 4bde3e90ee98
children 868cf39d9b15
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0:4bde3e90ee98 1:196e13c09881
36 36
37 python '$__tool_directory__/CreateAssemblyPicklists_script.py' 37 python '$__tool_directory__/CreateAssemblyPicklists_script.py'
38 --parts_files '$renamed_paths' 38 --parts_files '$renamed_paths'
39 --picklist '$picklist' 39 --picklist '$picklist'
40 --source_plate 'source_plate.xlsx' 40 --source_plate 'source_plate.xlsx'
41 --backbone_name '$backbone_name' 41 --backbone_name '$adv.backbone_name'
42 --part_backbone_ratio '$part_backbone_ratio' 42 --part_backbone_ratio '$adv.part_backbone_ratio'
43 --quantity_unit '$quantity_unit' 43 --quantity_unit '$quantity_unit'
44 --part_quantity '$part_quantity' 44 --part_quantity '$part_quantity'
45 --buffer_volume '$buffer_volume' 45 --buffer_volume '$buffer_volume'
46 --total_volume '$total_volume' 46 --total_volume '$total_volume'
47 --dispenser '$dispenser' 47 --dispenser '$dispenser'
48 --result_zip 'picklist.zip' && 48 --result_zip 'picklist.zip' &&
49 cp 'picklist.zip' '$output_zip' 49 cp 'picklist.zip' '$output_zip'
50 ]]></command> 50 ]]></command>
51 <inputs> 51 <inputs>
52 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/> 52 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" />
53 <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/> 53 <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/>
54 <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/> 54 <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/>
55 <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" />
56 <param name="part_backbone_ratio" type="float" max="1.0" label="Backbone Name(s)" />
57 <param name="quantity_unit" type="select" label="Part quantity unit"> 55 <param name="quantity_unit" type="select" label="Part quantity unit">
58 <option value="fmol" selected="true">femto-mole</option> 56 <option value="fmol" selected="true">femto-mole</option>
59 <option value="nM">nano-molar</option> 57 <option value="nM">nano-molar</option>
60 <option value="ng">nano-gram</option> 58 <option value="ng">nano-gram</option>
61 </param> 59 </param>
64 <param name="total_volume" type="float" value="1.0" label="Total volume (µL)" /> 62 <param name="total_volume" type="float" value="1.0" label="Total volume (µL)" />
65 <param name="dispenser" type="select" label="Dispenser Machine"> 63 <param name="dispenser" type="select" label="Dispenser Machine">
66 <option value="labcyte_echo" selected="true">Labcyte ECHO</option> 64 <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
67 <option value="tecan_evo">Tecab EVO</option> 65 <option value="tecan_evo">Tecab EVO</option>
68 </param> 66 </param>
67 <section name="adv" title="advance" expanded="false">
68 <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" optional='true'/>
69 <param name="part_backbone_ratio" type="float" value='1.0' max="1.0" label="Backbone Molar Ratio" optional='true' />
70 </section>
69 </inputs> 71 </inputs>
70 <outputs> 72 <outputs>
71 <data format="zip" name="output_zip" label="picklist (zip)"/> 73 <data format="zip" name="output_zip" label="picklist (zip)"/>
72 </outputs> 74 </outputs>
73 <tests> 75 <tests>
169 <element name="p9_puror" value="emma_parts/p9_puror.gb" /> 171 <element name="p9_puror" value="emma_parts/p9_puror.gb" />
170 </collection> 172 </collection>
171 </param> 173 </param>
172 <param name="picklist" value="example_picklist.xls" /> 174 <param name="picklist" value="example_picklist.xls" />
173 <param name="source_plate" value="example_echo_plate.xlsx"/> 175 <param name="source_plate" value="example_echo_plate.xlsx"/>
174 <param name="backbone_name" value="HC_Amp_ccdB" />
175 <param name="part_backbone_ratio" value="1" />
176 <param name="quantity_unit" value="fmol" /> 176 <param name="quantity_unit" value="fmol" />
177 <param name="part_quantity" value="1.3" /> 177 <param name="part_quantity" value="1.3" />
178 <param name="buffer_volume" value="0.3" /> 178 <param name="buffer_volume" value="0.3" />
179 <param name="total_volume" value="1.0" /> 179 <param name="total_volume" value="1.0" />
180 <param name="dispenser" value="labcyte_echo" /> 180 <param name="dispenser" value="labcyte_echo" />
191 ========================= 191 =========================
192 192
193 Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo. 193 Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo.
194 `Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_ 194 `Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_
195 195
196 **Advance parameter**:
197 ---------------------
198 * **Backbone Name(s)**: It can be one backbone or more than one (one name by line)
199 * **Backbone Molar Ratio**: between 0.0 and 1.0
200 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.
201 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case.
196 ]]></help> 202 ]]></help>
197 <citations> 203 <citations>
198 <citation type="bibtex"> 204 <citation type="bibtex">
199 @unpublished{create_assembly_picklists 205 @unpublished{create_assembly_picklists
200 author = {Ramiz Khaled}, 206 author = {Ramiz Khaled},