Mercurial > repos > tduigou > create_assembly_picklists

comparison create_assembly_picklists.xml @ 4:0b8f66f0383a 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 11:55:14 +0000
parents 9f9bb8d0dd4e
children bb70a954048e
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3:9f9bb8d0dd4e 4:0b8f66f0383a
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 '$adv.backbone_name' 41 --backbone_name '$setting.adv.backbone_name'
42 --part_backbone_ratio '$adv.part_backbone_ratio' 42 --part_backbone_ratio '$setting.adv.part_backbone_ratio'
43 --quantity_unit '$quantity_unit' 43 --quantity_unit '$setting.quantity_unit'
44 --part_quantity '$part_quantity' 44 --part_quantity '$setting.part_quantity'
45 --buffer_volume '$buffer_volume' 45 --buffer_volume '$setting.buffer_volume'
46 --total_volume '$total_volume' 46 --total_volume '$setting.total_volume'
47 --dispenser '$dispenser' 47 --dispenser '$setting.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 <conditional name='setting'>
53 <param name="mode" type="select" label="Mode">
54 <option value="std" selected="true">Standard</option>
55 <option value="demo">DEMO</option>
56 </param>
57 <when value="std">
58 <param name="quantity_unit" type="select" label="Part quantity unit">
59 <option value="fmol" selected="true">femto-mole</option>
60 <option value="nM">nano-molar</option>
61 <option value="ng">nano-gram</option>
62 </param>
63 <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
64 <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
65 <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
66 <param name="dispenser" type="select" label="Dispenser Machine">
67 <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
68 <option value="tecan_evo">Tecab EVO</option>
69 </param>
70 <section name="adv" title="advance" expanded="false">
71 <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" optional='true'/>
72 <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
73 </section>
74 </when>
75 <when value="demo">
76 <param name="quantity_unit" type="select" label="Part quantity unit">
77 <option value="fmol" selected="true">femto-mole</option>
78 <option value="nM">nano-molar</option>
79 <option value="ng">nano-gram</option>
80 </param>
81 <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
82 <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
83 <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
84 <param name="dispenser" type="select" label="Dispenser Machine">
85 <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
86 <option value="tecan_evo">Tecab EVO</option>
87 </param>
88 <section name="adv" title="advance" expanded="false">
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' />
91 </section>
92 </when>
93 </conditional>
52 <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 and/or Fasta File(s)" />
53 <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)"/>
54 <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)"/>
55 <param name="quantity_unit" type="select" label="Part quantity unit">
56 <option value="fmol" selected="true">femto-mole</option>
57 <option value="nM">nano-molar</option>
58 <option value="ng">nano-gram</option>
59 </param>
60 <param name="part_quantity" type="float" value="1.3" min="0" label="Part quantity" />
61 <param name="buffer_volume" type="float" value="0.3" min="0" label="Buffer volume (µL)" />
62 <param name="total_volume" type="float" value="1.0" min="0" label="Total volume (µL)" />
63 <param name="dispenser" type="select" label="Dispenser Machine">
64 <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
65 <option value="tecan_evo">Tecab EVO</option>
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' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
70 </section>
71 </inputs> 97 </inputs>
72 <outputs> 98 <outputs>
73 <data format="zip" name="output_zip" label="picklist (zip)"/> 99 <data format="zip" name="output_zip" label="picklist (zip)"/>
74 </outputs> 100 </outputs>
75 <tests> 101 <tests>
171 <element name="p9_puror" value="emma_parts/p9_puror.gb" /> 197 <element name="p9_puror" value="emma_parts/p9_puror.gb" />
172 </collection> 198 </collection>
173 </param> 199 </param>
174 <param name="picklist" value="example_picklist.xls" /> 200 <param name="picklist" value="example_picklist.xls" />
175 <param name="source_plate" value="example_echo_plate.xlsx"/> 201 <param name="source_plate" value="example_echo_plate.xlsx"/>
176 <param name="quantity_unit" value="fmol" /> 202 <conditional name='setting'>
177 <param name="part_quantity" value="1.3" /> 203 <param name="mode" value="std" />
178 <param name="buffer_volume" value="0.3" /> 204 <param name="quantity_unit" value="fmol" />
179 <param name="total_volume" value="1.0" /> 205 <param name="part_quantity" value="1.3" />
180 <param name="dispenser" value="labcyte_echo" /> 206 <param name="buffer_volume" value="0.3" />
207 <param name="total_volume" value="1.0" />
208 <param name="dispenser" value="labcyte_echo" />
209 </conditional>
210 <output name="output_zip" ftype='zip'>
211 <assert_contents>
212 <has_archive_member path=".*" n="5"/>
213 </assert_contents>
214 </output>
215 </test>
216 <!--test demo-->
217 <test>
218 <param name="genbank_files">
219 <collection type="list">
220 <element name="HC_Amp_ccdB" value="emma_parts/HC_Amp_ccdB.gb" />
221 <element name="conn a-c" value="emma_parts/conn a-c.gb" />
222 <element name="conn b-e" value="emma_parts/conn b-e.gb" />
223 <element name="conn b-l" value="emma_parts/conn b-l.gb" />
224 <element name="conn d-e" value="emma_parts/conn d-e.gb" />
225 <element name="conn d-f" value="emma_parts/conn d-f.gb" />
226 <element name="conn h-ha" value="emma_parts/conn h-ha.gb" />
227 <element name="conn h-j" value="emma_parts/conn h-j.gb" />
228 <element name="conn h-k" value="emma_parts/conn h-k.gb" />
229 <element name="conn j-k" value="emma_parts/conn j-k.gb" />
230 <element name="conn l-n" value="emma_parts/conn l-n.gb" />
231 <element name="conn l-r" value="emma_parts/conn l-r.gb" />
232 <element name="conn l-w" value="emma_parts/conn l-w.gb" />
233 <element name="conn l-y" value="emma_parts/conn l-y.gb" />
234 <element name="conn q-r" value="emma_parts/conn q-r.gb" />
235 <element name="conn r-w" value="emma_parts/conn r-w.gb" />
236 <element name="conn t-v" value="emma_parts/conn t-v.gb" />
237 <element name="conn w-x" value="emma_parts/conn w-x.gb" />
238 <element name="conn w-y" value="emma_parts/conn w-y.gb" />
239 <element name="conn w-z" value="emma_parts/conn w-z.gb" />
240 <element name="conn y-z" value="emma_parts/conn y-z.gb" />
241 <element name="p10_tet-aptazyme" value="emma_parts/p10_tet-aptazyme.gb" />
242 <element name="p11_sv40polya" value="emma_parts/p11_sv40polya.gb" />
243 <element name="p14_cmvp" value="emma_parts/p14_cmvp.gb" />
244 <element name="p14_sv40p" value="emma_parts/p14_sv40p.gb" />
245 <element name="p15_puror" value="emma_parts/p15_puror.gb" />
246 <element name="p16_bghpolya" value="emma_parts/p16_bghpolya.gb" />
247 <element name="p18_cmvp" value="emma_parts/p18_cmvp.gb" />
248 <element name="p18_ef1ap" value="emma_parts/p18_ef1ap.gb" />
249 <element name="p19_mneogreen" value="emma_parts/p19_mneogreen.gb" />
250 <element name="p19_mruby2" value="emma_parts/p19_mruby2.gb" />
251 <element name="p19_mtagbfp2" value="emma_parts/p19_mtagbfp2.gb" />
252 <element name="p19_tet-on-3g" value="emma_parts/p19_tet-on-3g.gb" />
253 <element name="p1_5'-itr-pb" value="emma_parts/p1_5'-itr-pb.gb" />
254 <element name="p1_5'ha-haavs1" value="emma_parts/p1_5'ha-haavs1.gb" />
255 <element name="p20_ct-minute-nes" value="emma_parts/p20_ct-minute-nes.gb" />
256 <element name="p20_ct-nes" value="emma_parts/p20_ct-nes.gb" />
257 <element name="p20_linker3" value="emma_parts/p20_linker3.gb" />
258 <element name="p20_p2a" value="emma_parts/p20_p2a.gb" />
259 <element name="p21_dmra" value="emma_parts/p21_dmra.gb" />
260 <element name="p21_mkate2" value="emma_parts/p21_mkate2.gb" />
261 <element name="p21_mneogreen" value="emma_parts/p21_mneogreen.gb" />
262 <element name="p21_mruby2" value="emma_parts/p21_mruby2.gb" />
263 <element name="p21_mtagbfp2" value="emma_parts/p21_mtagbfp2.gb" />
264 <element name="p21_puror" value="emma_parts/p21_puror.gb" />
265 <element name="p22_pgkpolya" value="emma_parts/p22_pgkpolya.gb" />
266 <element name="p23_insulatorfb" value="emma_parts/p23_insulatorfb.gb" />
267 <element name="p24_3'ha_haavs1" value="emma_parts/p24_3'ha_haavs1.gb" />
268 <element name="p24_3'pb" value="emma_parts/p24_3'pb.gb" />
269 <element name="p25_sv40-ori" value="emma_parts/p25_sv40-ori.gb" />
270 <element name="p2_insulatorfb" value="emma_parts/p2_insulatorfb.gb" />
271 <element name="p3_cagp" value="emma_parts/p3_cagp.gb" />
272 <element name="p3_cmvp_tet" value="emma_parts/p3_cmvp_tet.gb" />
273 <element name="p3_ef1ap" value="emma_parts/p3_ef1ap.gb" />
274 <element name="p3_tre3gp" value="emma_parts/p3_tre3gp.gb" />
275 <element name="p4_kt-l7ae -weiss" value="emma_parts/p4_kt-l7ae -weiss.gb" />
276 <element name="p4_lac-o" value="emma_parts/p4_lac-o.gb" />
277 <element name="p5_attb-bxb1" value="emma_parts/p5_attb-bxb1.gb" />
278 <element name="p5_attp-bxb1" value="emma_parts/p5_attp-bxb1.gb" />
279 <element name="p5_k1-k1" value="emma_parts/p5_k1-k1.gb" />
280 <element name="p5_kt-weiss" value="emma_parts/p5_kt-weiss.gb" />
281 <element name="p6_atg_boxc" value="emma_parts/p6_atg_boxc.gb" />
282 <element name="p6_kozak-atg" value="emma_parts/p6_kozak-atg.gb" />
283 <element name="p6_nt-igkl sequence" value="emma_parts/p6_nt-igkl sequence.gb" />
284 <element name="p6_nt-mls" value="emma_parts/p6_nt-mls.gb" />
285 <element name="p6_nt-myristoylation signal" value="emma_parts/p6_nt-myristoylation signal.gb" />
286 <element name="p6_nt-palm sequence" value="emma_parts/p6_nt-palm sequence.gb" />
287 <element name="p6_nt-sv40_nls" value="emma_parts/p6_nt-sv40_nls.gb" />
288 <element name="p7_bxb1" value="emma_parts/p7_bxb1.gb" />
289 <element name="p7_l7ae-weiss" value="emma_parts/p7_l7ae-weiss.gb" />
290 <element name="p7_l7ae" value="emma_parts/p7_l7ae.gb" />
291 <element name="p7_laci" value="emma_parts/p7_laci.gb" />
292 <element name="p7_mcherry" value="emma_parts/p7_mcherry.gb" />
293 <element name="p7_mkate2" value="emma_parts/p7_mkate2.gb" />
294 <element name="p7_mneogreen" value="emma_parts/p7_mneogreen.gb" />
295 <element name="p7_mruby2" value="emma_parts/p7_mruby2.gb" />
296 <element name="p7_mtagbfp2" value="emma_parts/p7_mtagbfp2.gb" />
297 <element name="p8_linker1" value="emma_parts/p8_linker1.gb" />
298 <element name="p8_linker2" value="emma_parts/p8_linker2.gb" />
299 <element name="p8_p2a" value="emma_parts/p8_p2a.gb" />
300 <element name="p8a_ct-kdel" value="emma_parts/p8a_ct-kdel.gb" />
301 <element name="p8b_ires2" value="emma_parts/p8b_ires2.gb" />
302 <element name="p9_a-tubulin" value="emma_parts/p9_a-tubulin.gb" />
303 <element name="p9_bsdr" value="emma_parts/p9_bsdr.gb" />
304 <element name="p9_dmrc" value="emma_parts/p9_dmrc.gb" />
305 <element name="p9_firefly luciferase" value="emma_parts/p9_firefly luciferase.gb" />
306 <element name="p9_mneogreen" value="emma_parts/p9_mneogreen.gb" />
307 <element name="p9_mruby2" value="emma_parts/p9_mruby2.gb" />
308 <element name="p9_mtagbfp2" value="emma_parts/p9_mtagbfp2.gb" />
309 <element name="p9_neor" value="emma_parts/p9_neor.gb" />
310 <element name="p9_puror" value="emma_parts/p9_puror.gb" />
311 </collection>
312 </param>
313 <param name="picklist" value="example_picklist.xls" />
314 <param name="source_plate" value="example_echo_plate.xlsx"/>
315 <conditional name='setting'>
316 <param name="mode" value="demo" />
317 </conditional>
181 <output name="output_zip" ftype='zip'> 318 <output name="output_zip" ftype='zip'>
182 <assert_contents> 319 <assert_contents>
183 <has_archive_member path=".*" n="5"/> 320 <has_archive_member path=".*" n="5"/>
184 </assert_contents> 321 </assert_contents>
185 </output> 322 </output>