Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 30:14b1c52fae62 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:30:58 -0500
parents 793f87231d49
children eb15a3841da4
comparison
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29:793f87231d49 30:14b1c52fae62
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