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comparison cloning_similation.xml @ 3:044d36066cb3 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 16 May 2025 12:40:59 +0000
parents 3171db614963
children 254d284a5be9
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2:3171db614963 3:044d36066cb3
36 --outdir_simulation 'outdir_zip' 36 --outdir_simulation 'outdir_zip'
37 --outdir_gb 'outdir_gb' 37 --outdir_gb 'outdir_gb'
38 --output_simulation 'output_zip.zip' 38 --output_simulation 'output_zip.zip'
39 --enzyme '$adv.enzyme' 39 --enzyme '$adv.enzyme'
40 --topology '$topology'&& 40 --topology '$topology'&&
41 cp 'output_zip.zip' '$output_zip' 41 cp 'output_zip.zip' '$output_zip'
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)"/> 44 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)"/>
45 <param name="assembly_csv" type="data" format="csv" label="assemnby csv"/> 45 <param name="assembly_csv" type="data" format="csv" label="assemnby csv"/>
46 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" value="None" optional="True"/> 46 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" value="None" optional="True"/>
95 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 95 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
96 <has_size min="5"/> 96 <has_size min="5"/>
97 </has_archive_member> 97 </has_archive_member>
98 </assert_contents> 98 </assert_contents>
99 </output> 99 </output>
100 <output_collection name="outdir_gb" type="list" count="4"> 100 <output_collection name="construct_gb" type="list" count="4">
101 <element name="construct_1"> 101 <element name="construct_1">
102 <assert_contents> 102 <assert_contents>
103 <has_n_lines min="20" /> 103 <has_n_lines min="20" />
104 </assert_contents> 104 </assert_contents>
105 </element> 105 </element>
137 <has_archive_member path="assambly_simulation/Report.pdf"> 137 <has_archive_member path="assambly_simulation/Report.pdf">
138 <has_size min="5"/> 138 <has_size min="5"/>
139 </has_archive_member> 139 </has_archive_member>
140 </assert_contents> 140 </assert_contents>
141 </output> 141 </output>
142 <output_collection name="outdir_gb" type="list" count="4"> 142 <output_collection name="construct_gb" type="list" count="3">
143 <element name="construct_1"> 143 <element name="construct_1">
144 <assert_contents> 144 <assert_contents>
145 <has_n_lines min="20" /> 145 <has_n_lines min="20" />
146 </assert_contents> 146 </assert_contents>
147 </element> 147 </element>
175 <has_archive_member path="assambly_simulation/Report.pdf"> 175 <has_archive_member path="assambly_simulation/Report.pdf">
176 <has_size min="5"/> 176 <has_size min="5"/>
177 </has_archive_member> 177 </has_archive_member>
178 </assert_contents> 178 </assert_contents>
179 </output> 179 </output>
180 <output_collection name="outdir_gb" type="list" count="0"> 180 <output_collection name="construct_gb" type="list" count="0">
181 </output_collection> 181 </output_collection>
182 </test> 182 </test>
183 <!--test BASIC_assembly class--> 183 <!--test BASIC_assembly class-->
184 <test> 184 <test>
185 <param name="genbank_files"> 185 <param name="genbank_files">
201 <has_archive_member path="assambly_simulation/Report.pdf"> 201 <has_archive_member path="assambly_simulation/Report.pdf">
202 <has_size min="5"/> 202 <has_size min="5"/>
203 </has_archive_member> 203 </has_archive_member>
204 </assert_contents> 204 </assert_contents>
205 </output> 205 </output>
206 <output_collection name="outdir_gb" type="list" count="0"> 206 <output_collection name="construct_gb" type="list" count="0">
207 </output_collection> 207 </output_collection>
208 </test> 208 </test>
209 <!--test biobrick_assembly class--> 209 <!--test biobrick_assembly class-->
210 <test> 210 <test>
211 <param name="genbank_files"> 211 <param name="genbank_files">
227 <has_archive_member path="assambly_simulation/Report.pdf"> 227 <has_archive_member path="assambly_simulation/Report.pdf">
228 <has_size min="5"/> 228 <has_size min="5"/>
229 </has_archive_member> 229 </has_archive_member>
230 </assert_contents> 230 </assert_contents>
231 </output> 231 </output>
232 <output_collection name="outdir_gb" type="list" count="0"> 232 <output_collection name="construct_gb" type="list" count="3">
233 <element name="C1_prom_barcode">
234 <assert_contents>
235 <has_n_lines min="20" />
236 </assert_contents>
237 </element>
238 <element name="C2_gfp_term">
239 <assert_contents>
240 <has_n_lines min="20" />
241 </assert_contents>
242 </element>
243 <element name="C3_final">
244 <assert_contents>
245 <has_n_lines min="20" />
246 </assert_contents>
247 </element>
233 </output_collection> 248 </output_collection>
234 </test> 249 </test>
235 <!--test type2s_assembly with domesticated files--> 250 <!--test type2s_assembly with domesticated files-->
236 <test> 251 <test>
237 <param name="genbank_files"> 252 <param name="genbank_files">
264 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 279 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
265 <has_size min="5"/> 280 <has_size min="5"/>
266 </has_archive_member> 281 </has_archive_member>
267 </assert_contents> 282 </assert_contents>
268 </output> 283 </output>
269 <output_collection name="outdir_gb" type="list" count="4"> 284 <output_collection name="construct_gb" type="list" count="4">
270 <element name="construct_1"> 285 <element name="construct_1">
271 <assert_contents> 286 <assert_contents>
272 <has_n_lines min="20" /> 287 <has_n_lines min="20" />
273 </assert_contents> 288 </assert_contents>
274 </element> 289 </element>