Mercurial > repos > lecorguille > xcms_xcmsset
comparison abims_xcms_xcmsSet.xml @ 30:14b1c52fae62 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author | workflow4metabolomics |
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date | Wed, 12 Feb 2020 08:30:58 -0500 |
parents | 793f87231d49 |
children | eb15a3841da4 |
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29:793f87231d49 | 30:14b1c52fae62 |
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1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.2"> | 1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> |
2 <description>Chromatographic peak detection</description> | 2 <description>Chromatographic peak detection</description> |
3 | 3 |
4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 <import>macros_xcms.xml</import> | 6 <import>macros_xcms.xml</import> |
222 <conditional name="methods"> | 222 <conditional name="methods"> |
223 <param name="method" value="CentWave" /> | 223 <param name="method" value="CentWave" /> |
224 <param name="ppm" value="25" /> | 224 <param name="ppm" value="25" /> |
225 <param name="peakwidth" value="20,50" /> | 225 <param name="peakwidth" value="20,50" /> |
226 </conditional> | 226 </conditional> |
227 <expand macro="test_file_load_single_ko15"/> | 227 <expand macro="test_file_load_single_file" filename="ko15"/> |
228 <assert_stdout> | 228 <assert_stdout> |
229 <has_text text="ppm: 25" /> | 229 <has_text text="ppm: 25" /> |
230 <has_text text="peakwidth: 20, 50" /> | 230 <has_text text="peakwidth: 20, 50" /> |
231 <has_text text="object with 1 samples" /> | 231 <has_text text="object with 1 samples" /> |
232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" /> | 232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" /> |
233 <has_text text="Mass range: 200.2-600 m/z" /> | 233 <has_text text="Mass range: 200.2-600 m/z" /> |
234 <has_text text="Peaks: 2262 (about 2262 per sample)" /> | 234 <has_text text="Peaks: 2262 (about 2262 per sample)" /> |
235 <has_text text="Peak Groups: 0" /> | 235 <has_text text="Peak Groups: 0" /> |
236 <has_text text="Sample classes: ." /> | 236 <has_text text="Sample classes: ." /> |
237 </assert_stdout> | 237 </assert_stdout> |
238 <!--<output name="xsetRData" file="ko15-xset.RData" />--> | |
238 </test> | 239 </test> |
239 <!-- DISABLE FOR TRAVIS | 240 <!-- DISABLE FOR TRAVIS |
240 Useful to generate test-data for the further steps | 241 Useful to generate test-data for the further steps |
241 <test> | 242 <test> |
242 <param name="image" value="ko16-raw.RData" ftype="rdata" /> | 243 <param name="image" value="ko16-raw.RData" ftype="rdata" /> |
243 <conditional name="methods"> | 244 <conditional name="methods"> |
244 <param name="method" value="CentWave" /> | 245 <param name="method" value="CentWave" /> |
245 <param name="ppm" value="25" /> | 246 <param name="ppm" value="25" /> |
246 <param name="peakwidth" value="20,50" /> | 247 <param name="peakwidth" value="20,50" /> |
247 </conditional> | 248 </conditional> |
249 <expand macro="test_file_load_single_file" filename="ko16"/> | |
248 <assert_stdout> | 250 <assert_stdout> |
249 <has_text text="object with 1 samples" /> | 251 <has_text text="object with 1 samples" /> |
250 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" /> | 252 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" /> |
251 <has_text text="Mass range: 200.1-600 m/z" /> | 253 <has_text text="Mass range: 200.1-600 m/z" /> |
252 <has_text text="Peaks: 2408 (about 2408 per sample)" /> | 254 <has_text text="Peaks: 2408 (about 2408 per sample)" /> |
253 <has_text text="Peak Groups: 0" /> | 255 <has_text text="Peak Groups: 0" /> |
254 <has_text text="Sample classes: ." /> | 256 <has_text text="Sample classes: ." /> |
255 </assert_stdout> | 257 </assert_stdout> |
258 <output name="xsetRData" file="ko16-xset.RData" /> | |
256 </test> | 259 </test> |
257 <test> | 260 <test> |
258 <param name="image" value="wt15-raw.RData" ftype="rdata" /> | 261 <param name="image" value="wt15-raw.RData" ftype="rdata" /> |
259 <conditional name="methods"> | 262 <conditional name="methods"> |
260 <param name="method" value="CentWave" /> | 263 <param name="method" value="CentWave" /> |
261 <param name="ppm" value="25" /> | 264 <param name="ppm" value="25" /> |
262 <param name="peakwidth" value="20,50" /> | 265 <param name="peakwidth" value="20,50" /> |
263 </conditional> | 266 </conditional> |
267 <expand macro="test_file_load_single_file" filename="wt15"/> | |
264 <assert_stdout> | 268 <assert_stdout> |
265 <has_text text="object with 1 samples" /> | 269 <has_text text="object with 1 samples" /> |
266 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" /> | 270 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" /> |
267 <has_text text="Mass range: 200.2-599.8 m/z" /> | 271 <has_text text="Mass range: 200.2-599.8 m/z" /> |
268 <has_text text="Peaks: 2278 (about 2278 per sample)" /> | 272 <has_text text="Peaks: 2278 (about 2278 per sample)" /> |
269 <has_text text="Peak Groups: 0" /> | 273 <has_text text="Peak Groups: 0" /> |
270 <has_text text="Sample classes: ." /> | 274 <has_text text="Sample classes: ." /> |
271 </assert_stdout> | 275 </assert_stdout> |
276 <output name="xsetRData" file="wt15-xset.RData" /> | |
272 </test> | 277 </test> |
273 <test> | 278 <test> |
274 <param name="image" value="wt16-raw.RData" ftype="rdata" /> | 279 <param name="image" value="wt16-raw.RData" ftype="rdata" /> |
275 <conditional name="methods"> | 280 <conditional name="methods"> |
276 <param name="method" value="CentWave" /> | 281 <param name="method" value="CentWave" /> |
277 <param name="ppm" value="25" /> | 282 <param name="ppm" value="25" /> |
278 <param name="peakwidth" value="20,50" /> | 283 <param name="peakwidth" value="20,50" /> |
279 </conditional> | 284 </conditional> |
285 <expand macro="test_file_load_single_file" filename="wt16"/> | |
280 <assert_stdout> | 286 <assert_stdout> |
281 <has_text text="object with 1 samples" /> | 287 <has_text text="object with 1 samples" /> |
282 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" /> | 288 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" /> |
283 <has_text text="Mass range: 200.3-600 m/z" /> | 289 <has_text text="Mass range: 200.3-600 m/z" /> |
284 <has_text text="Peaks: 2303 (about 2303 per sample)" /> | 290 <has_text text="Peaks: 2303 (about 2303 per sample)" /> |
285 <has_text text="Peak Groups: 0" /> | 291 <has_text text="Peak Groups: 0" /> |
286 <has_text text="Sample classes: ." /> | 292 <has_text text="Sample classes: ." /> |
287 </assert_stdout> | 293 </assert_stdout> |
294 <output name="xsetRData" file="wt16-xset.RData" /> | |
288 </test> | 295 </test> |
289 --> | 296 --> |
290 <!-- DISABLE FOR TRAVIS | 297 <!-- DISABLE FOR TRAVIS |
291 Test to test the different methods parameters | 298 Test to test the different methods parameters |
292 <test> | 299 <test> |
483 Changelog/News | 490 Changelog/News |
484 -------------- | 491 -------------- |
485 | 492 |
486 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS | 493 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS |
487 | 494 |
495 @HELP_XCMS_NEWVERSION_3610@ | |
496 | |
488 **Version 3.4.4.1 - 30/04/2019** | 497 **Version 3.4.4.1 - 30/04/2019** |
489 | 498 |
490 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. | 499 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. |
491 | 500 |
492 **Version 3.4.4.0 - 08/02/2019** | 501 @HELP_XCMS_NEWVERSION_3440@ |
493 | |
494 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) | |
495 | |
496 | 502 |
497 **Version 3.0.0.0 - 08/03/2018** | 503 **Version 3.0.0.0 - 08/03/2018** |
498 | 504 |
499 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. | 505 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. |
500 | 506 |