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comparison cloning_similation.xml @ 2:3171db614963 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 11:32:06 +0000
parents 32e44a646b68
children 044d36066cb3
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1:32e44a646b68 2:3171db614963
22 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input]) 22 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
23 #else 23 #else
24 #set domesticated_input_paths = "" 24 #set domesticated_input_paths = ""
25 #set file_name_mapping_dom = "" 25 #set file_name_mapping_dom = ""
26 #end if 26 #end if
27 mkdir 'outdir_zip' && 27 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
28 python '$__tool_directory__/cloning_simulation.py' 28 python '$__tool_directory__/cloning_simulation.py'
29 --parts_files '$genbank_file_paths' 29 --parts_files '$genbank_file_paths'
30 --domesticated_seq '$domesticated_input_paths' 30 --domesticated_seq '$domesticated_input_paths'
31 --assembly_csv '$assembly_csv' 31 --assembly_csv '$assembly_csv'
32 --assembly_plan_name '$assembly_plan_name' 32 --assembly_plan_name '$assembly_plan_name'
33 --file_name_mapping '$file_name_mapping' 33 --file_name_mapping '$file_name_mapping'
34 --file_name_mapping_dom '$file_name_mapping_dom' 34 --file_name_mapping_dom '$file_name_mapping_dom'
35 --use_file_names_as_id '$adv.use_file_names_as_ids' 35 --use_file_names_as_id '$adv.use_file_names_as_ids'
36 --outdir_simulation 'outdir_zip' 36 --outdir_simulation 'outdir_zip'
37 --outdir_gb 'outdir_gb'
37 --output_simulation 'output_zip.zip' 38 --output_simulation 'output_zip.zip'
38 --enzyme '$adv.enzyme' 39 --enzyme '$adv.enzyme'
39 --topology '$topology'&& 40 --topology '$topology'&&
40 cp 'output_zip.zip' '$output_zip' 41 cp 'output_zip.zip' '$output_zip'
41 ]]></command> 42 ]]></command>
59 <param name="enzyme" type="text" label="restrintion enzyme" value="auto" optional="True"/> 60 <param name="enzyme" type="text" label="restrintion enzyme" value="auto" optional="True"/>
60 </section> 61 </section>
61 </inputs> 62 </inputs>
62 <outputs> 63 <outputs>
63 <data format="zip" name="output_zip" label="simulation results"/> 64 <data format="zip" name="output_zip" label="simulation results"/>
65 <collection name="construct_gb" type="list" label="All constrauct GenBank">
66 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
67 </collection>
64 </outputs> 68 </outputs>
65 <tests> 69 <tests>
66 <!--test type2s_assembly class--> 70 <!--test type2s_assembly class-->
67 <test> 71 <test>
68 <param name="genbank_files"> 72 <param name="genbank_files">
91 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 95 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
92 <has_size min="5"/> 96 <has_size min="5"/>
93 </has_archive_member> 97 </has_archive_member>
94 </assert_contents> 98 </assert_contents>
95 </output> 99 </output>
100 <output_collection name="outdir_gb" type="list" count="4">
101 <element name="construct_1">
102 <assert_contents>
103 <has_n_lines min="20" />
104 </assert_contents>
105 </element>
106 <element name="construct_2">
107 <assert_contents>
108 <has_n_lines min="20" />
109 </assert_contents>
110 </element>
111 <element name="construct_3">
112 <assert_contents>
113 <has_n_lines min="20" />
114 </assert_contents>
115 </element>
116 <element name="construct_4">
117 <assert_contents>
118 <has_n_lines min="20" />
119 </assert_contents>
120 </element>
121 </output_collection>
96 </test> 122 </test>
97 <!--test gibson_assembly class--> 123 <!--test gibson_assembly class-->
98 <test> 124 <test>
99 <param name="genbank_files"> 125 <param name="genbank_files">
100 <collection type="list"> 126 <collection type="list">
111 <has_archive_member path="assambly_simulation/Report.pdf"> 137 <has_archive_member path="assambly_simulation/Report.pdf">
112 <has_size min="5"/> 138 <has_size min="5"/>
113 </has_archive_member> 139 </has_archive_member>
114 </assert_contents> 140 </assert_contents>
115 </output> 141 </output>
142 <output_collection name="outdir_gb" type="list" count="4">
143 <element name="construct_1">
144 <assert_contents>
145 <has_n_lines min="20" />
146 </assert_contents>
147 </element>
148 <element name="construct_2">
149 <assert_contents>
150 <has_n_lines min="20" />
151 </assert_contents>
152 </element>
153 <element name="construct_3">
154 <assert_contents>
155 <has_n_lines min="20" />
156 </assert_contents>
157 </element>
158 </output_collection>
116 </test> 159 </test>
117 <!--test lcr_assembly class--> 160 <!--test lcr_assembly class-->
118 <test> 161 <test>
119 <param name="genbank_files"> 162 <param name="genbank_files">
120 <collection type="list"> 163 <collection type="list">
132 <has_archive_member path="assambly_simulation/Report.pdf"> 175 <has_archive_member path="assambly_simulation/Report.pdf">
133 <has_size min="5"/> 176 <has_size min="5"/>
134 </has_archive_member> 177 </has_archive_member>
135 </assert_contents> 178 </assert_contents>
136 </output> 179 </output>
180 <output_collection name="outdir_gb" type="list" count="0">
181 </output_collection>
137 </test> 182 </test>
138 <!--test BASIC_assembly class--> 183 <!--test BASIC_assembly class-->
139 <test> 184 <test>
140 <param name="genbank_files"> 185 <param name="genbank_files">
141 <collection type="list"> 186 <collection type="list">
156 <has_archive_member path="assambly_simulation/Report.pdf"> 201 <has_archive_member path="assambly_simulation/Report.pdf">
157 <has_size min="5"/> 202 <has_size min="5"/>
158 </has_archive_member> 203 </has_archive_member>
159 </assert_contents> 204 </assert_contents>
160 </output> 205 </output>
206 <output_collection name="outdir_gb" type="list" count="0">
207 </output_collection>
161 </test> 208 </test>
162 <!--test biobrick_assembly class--> 209 <!--test biobrick_assembly class-->
163 <test> 210 <test>
164 <param name="genbank_files"> 211 <param name="genbank_files">
165 <collection type="list"> 212 <collection type="list">
180 <has_archive_member path="assambly_simulation/Report.pdf"> 227 <has_archive_member path="assambly_simulation/Report.pdf">
181 <has_size min="5"/> 228 <has_size min="5"/>
182 </has_archive_member> 229 </has_archive_member>
183 </assert_contents> 230 </assert_contents>
184 </output> 231 </output>
232 <output_collection name="outdir_gb" type="list" count="0">
233 </output_collection>
185 </test> 234 </test>
186 <!--test type2s_assembly with domesticated files--> 235 <!--test type2s_assembly with domesticated files-->
187 <test> 236 <test>
188 <param name="genbank_files"> 237 <param name="genbank_files">
189 <collection type="list"> 238 <collection type="list">
215 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 264 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
216 <has_size min="5"/> 265 <has_size min="5"/>
217 </has_archive_member> 266 </has_archive_member>
218 </assert_contents> 267 </assert_contents>
219 </output> 268 </output>
269 <output_collection name="outdir_gb" type="list" count="4">
270 <element name="construct_1">
271 <assert_contents>
272 <has_n_lines min="20" />
273 </assert_contents>
274 </element>
275 <element name="construct_2">
276 <assert_contents>
277 <has_n_lines min="20" />
278 </assert_contents>
279 </element>
280 <element name="construct_3">
281 <assert_contents>
282 <has_n_lines min="20" />
283 </assert_contents>
284 </element>
285 <element name="construct_4">
286 <assert_contents>
287 <has_n_lines min="20" />
288 </assert_contents>
289 </element>
290 </output_collection>
220 </test> 291 </test>
221 </tests> 292 </tests>
222 293
223 <help><![CDATA[ 294 <help><![CDATA[
224 Cloning_Simulation 295 Cloning_Simulation