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comparison seq_form_db.xml @ 2:11a3752feb0a draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 7f5d8b62d749a0c41110cd9c04e0254e4fd44893-dirty
author tduigou
date Wed, 15 Oct 2025 12:33:41 +0000
parents 7680420caf9f
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1:7680420caf9f 2:11a3752feb0a
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='missing fragments' />
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="0" />
129 </assert_contents>
130 </output>
124 </test> 131 </test>
125 <!--JSON parameters--> 132 <!--JSON parameters-->
126 <test> 133 <test>
127 <param name="input" value="2-step-golden_gate_plan.csv" /> 134 <param name="input" value="2-step-golden_gate_plan.csv" />
128 <conditional name="json_use"> 135 <conditional name="json_use">
189 <assert_contents> 196 <assert_contents>
190 <has_n_lines min="10" /> 197 <has_n_lines min="10" />
191 </assert_contents> 198 </assert_contents>
192 </element> 199 </element>
193 </output_collection> 200 </output_collection>
201 <output name='report'>
202 <assert_contents>
203 <has_n_lines n="0" />
204 </assert_contents>
205 </output>
206 </test>
207 <!--test missing fragments-->
208 <test>
209 <param name="input" value="test_missing_input.csv" />
210 <conditional name="json_use">
211 <param name='use_json_paramers' value='false' />
212 <param name="table" value="sample" />
213 <param name="sequence_column" value="sequence" />
214 <param name="annotation_columns" value="annotation" />
215 <param name="fragment_column" value="fragment" />
216 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
217 </conditional>
218 <output_collection name="output_gb" type="list" count="12">
219 <element name="part_A">
220 <assert_contents>
221 <has_n_lines min="10" />
222 </assert_contents>
223 </element>
224 <element name="part_B">
225 <assert_contents>
226 <has_n_lines min="10" />
227 </assert_contents>
228 </element>
229 <element name="part_C">
230 <assert_contents>
231 <has_n_lines min="10" />
232 </assert_contents>
233 </element>
234 <element name="part_D">
235 <assert_contents>
236 <has_n_lines min="10" />
237 </assert_contents>
238 </element>
239 <element name="part_E">
240 <assert_contents>
241 <has_n_lines min="10" />
242 </assert_contents>
243 </element>
244 <element name="part_F">
245 <assert_contents>
246 <has_n_lines min="10" />
247 </assert_contents>
248 </element>
249 <element name="part_G">
250 <assert_contents>
251 <has_n_lines min="10" />
252 </assert_contents>
253 </element>
254 <element name="part_H">
255 <assert_contents>
256 <has_n_lines min="10" />
257 </assert_contents>
258 </element>
259 <element name="part_I">
260 <assert_contents>
261 <has_n_lines min="10" />
262 </assert_contents>
263 </element>
264 <element name="part_J">
265 <assert_contents>
266 <has_n_lines min="10" />
267 </assert_contents>
268 </element>
269 <element name="part_K">
270 <assert_contents>
271 <has_n_lines min="10" />
272 </assert_contents>
273 </element>
274 <element name="part_L">
275 <assert_contents>
276 <has_n_lines min="10" />
277 </assert_contents>
278 </element>
279 </output_collection>
280 <output name='report'>
281 <assert_contents>
282 <has_n_lines n="6" />
283 <has_line_matching expression="ACP10001AaCbbBS" />
284 <has_line_matching expression="NEW20001BbDccKT" />
285 <has_line_matching expression="XYZ10003AaCbbBS" />
286 <has_line_matching expression="CFP10002AaCbbBS" />
287 <has_line_matching expression="ALT30005CcEddLM" />
288 <has_line_matching expression="QWE10004AaCbbBS" />
289 </assert_contents>
290 </output>
194 </test> 291 </test>
195 </tests> 292 </tests>
196 293
197 <help><![CDATA[ 294 <help><![CDATA[
198 Get sequences Data From DB 295 Get sequences Data From DB