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comparison seq_form_db.xml @ 1:54e716c11b71 draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
author tduigou
date Tue, 29 Jul 2025 12:01:32 +0000
parents 934050a8037e
children 3bb9bbecae97
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0:934050a8037e 1:54e716c11b71
1 <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Import fragment's data from an accessible DB and export it as .gb files</description> 2 <description>Import fragment's data from an accessible DB and export it as .gb files</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">2</token>
5 <token name="@TOOL_VERSION@">0.2.0</token> 5 <token name="@TOOL_VERSION@">0.3.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="2.2.3">pandas</requirement> 8 <requirement type="package" version="2.2.3">pandas</requirement>
9 <requirement type="package" version="2.0.40">sqlalchemy</requirement> 9 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
10 <requirement type="package" version="2.9.9">psycopg2</requirement> 10 <requirement type="package" version="2.9.9">psycopg2</requirement>
23 --fragment_column '$json_use.fragment_column' 23 --fragment_column '$json_use.fragment_column'
24 #else: 24 #else:
25 --json_conf '$json_use.json_conf' 25 --json_conf '$json_use.json_conf'
26 #end if 26 #end if
27 --output 'outdir' 27 --output 'outdir'
28 --report '$report'
28 ]]></command> 29 ]]></command>
29 <inputs> 30 <inputs>
30 <param name="input" type="data" format="csv" label="Input CSV File" /> 31 <param name="input" type="data" format="csv" label="Input CSV File" />
31 <conditional name="json_use"> 32 <conditional name="json_use">
32 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" /> 33 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <collection name="output_gb" type="list" label="GenBank Files collection" > 47 <collection name="output_gb" type="list" label="GenBank Files collection" >
47 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" /> 48 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
48 </collection> 49 </collection>
50 <data name='report' format='txt' label='text report' />
49 </outputs> 51 </outputs>
50 <tests> 52 <tests>
51 <!--manual parameters--> 53 <!--manual parameters-->
52 <test> 54 <test>
53 <param name="input" value="2-step-golden_gate_plan.csv" /> 55 <param name="input" value="2-step-golden_gate_plan.csv" />
119 <assert_contents> 121 <assert_contents>
120 <has_n_lines min="10" /> 122 <has_n_lines min="10" />
121 </assert_contents> 123 </assert_contents>
122 </element> 124 </element>
123 </output_collection> 125 </output_collection>
126 <output name='report'>
127 <assert_contents>
128 <has_n_lines n="1" />
129 <has_line_matching expression="NO missing fragments in DB" />
130 </assert_contents>
131 </output>
124 </test> 132 </test>
125 <!--JSON parameters--> 133 <!--JSON parameters-->
126 <test> 134 <test>
127 <param name="input" value="2-step-golden_gate_plan.csv" /> 135 <param name="input" value="2-step-golden_gate_plan.csv" />
128 <conditional name="json_use"> 136 <conditional name="json_use">
189 <assert_contents> 197 <assert_contents>
190 <has_n_lines min="10" /> 198 <has_n_lines min="10" />
191 </assert_contents> 199 </assert_contents>
192 </element> 200 </element>
193 </output_collection> 201 </output_collection>
202 <output name='report'>
203 <assert_contents>
204 <has_n_lines n="1" />
205 <has_line_matching expression="NO missing fragments in DB" />
206 </assert_contents>
207 </output>
208 </test>
209 <!--test missing fragments-->
210 <test>
211 <param name="input" value="test_missing_input.csv" />
212 <conditional name="json_use">
213 <param name='use_json_paramers' value='false' />
214 <param name="table" value="sample" />
215 <param name="sequence_column" value="sequence" />
216 <param name="annotation_columns" value="annotation" />
217 <param name="fragment_column" value="fragment" />
218 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
219 </conditional>
220 <output_collection name="output_gb" type="list" count="12">
221 <element name="part_A">
222 <assert_contents>
223 <has_n_lines min="10" />
224 </assert_contents>
225 </element>
226 <element name="part_B">
227 <assert_contents>
228 <has_n_lines min="10" />
229 </assert_contents>
230 </element>
231 <element name="part_C">
232 <assert_contents>
233 <has_n_lines min="10" />
234 </assert_contents>
235 </element>
236 <element name="part_D">
237 <assert_contents>
238 <has_n_lines min="10" />
239 </assert_contents>
240 </element>
241 <element name="part_E">
242 <assert_contents>
243 <has_n_lines min="10" />
244 </assert_contents>
245 </element>
246 <element name="part_F">
247 <assert_contents>
248 <has_n_lines min="10" />
249 </assert_contents>
250 </element>
251 <element name="part_G">
252 <assert_contents>
253 <has_n_lines min="10" />
254 </assert_contents>
255 </element>
256 <element name="part_H">
257 <assert_contents>
258 <has_n_lines min="10" />
259 </assert_contents>
260 </element>
261 <element name="part_I">
262 <assert_contents>
263 <has_n_lines min="10" />
264 </assert_contents>
265 </element>
266 <element name="part_J">
267 <assert_contents>
268 <has_n_lines min="10" />
269 </assert_contents>
270 </element>
271 <element name="part_K">
272 <assert_contents>
273 <has_n_lines min="10" />
274 </assert_contents>
275 </element>
276 <element name="part_L">
277 <assert_contents>
278 <has_n_lines min="10" />
279 </assert_contents>
280 </element>
281 </output_collection>
282 <output name='report'>
283 <assert_contents>
284 <has_n_lines n="7" />
285 <has_line_matching expression="Missing fragment in DB:" />
286 <has_line_matching expression="ACP10001AaCbbBS" />
287 <has_line_matching expression="NEW20001BbDccKT" />
288 <has_line_matching expression="XYZ10003AaCbbBS" />
289 <has_line_matching expression="CFP10002AaCbbBS" />
290 <has_line_matching expression="ALT30005CcEddLM" />
291 <has_line_matching expression="QWE10004AaCbbBS" />
292 </assert_contents>
293 </output>
194 </test> 294 </test>
195 </tests> 295 </tests>
196 296
197 <help><![CDATA[ 297 <help><![CDATA[
198 Get sequences Data From DB 298 Get sequences Data From DB