Mercurial > repos > lecorguille > xcms_group
comparison abims_xcms_group.xml @ 27:d45a786cbc40 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author | workflow4metabolomics |
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date | Wed, 07 Apr 2021 12:06:33 +0000 |
parents | 0d05d0458376 |
children | 2b676d5eb848 |
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26:0d05d0458376 | 27:d45a786cbc40 |
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1 <tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy2"> | 1 <tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy0"> |
2 | 2 |
3 <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> | 3 <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> |
4 | 4 |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
83 <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.groupChromPeaks.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/> | 83 <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.groupChromPeaks.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/> |
84 <expand macro="output_peaklist" function="group"/> | 84 <expand macro="output_peaklist" function="group"/> |
85 </outputs> | 85 </outputs> |
86 | 86 |
87 <tests> | 87 <tests> |
88 <!-- from xcmsSet | 88 <!-- from merge --> |
89 <!-- DISABLE FOR TRAVIS but useful in order to REFRESH TEST-DATA | |
89 <test> | 90 <test> |
90 <param name="image" value="faahKO-single-class.xset.merged.RData" ftype="rdata"/> | 91 <param name="image" value="faahKO-single-class.xset.merged.RData" ftype="rdata"/> |
91 <conditional name="methods"> | 92 <conditional name="methods"> |
92 <param name="method" value="PeakDensity"/> | 93 <param name="method" value="PeakDensity"/> |
93 <param name="bw" value="5"/> | 94 <param name="bw" value="5"/> |
201 </assert_stdout> | 202 </assert_stdout> |
202 </test> | 203 </test> |
203 --> | 204 --> |
204 <!-- from retcor --> | 205 <!-- from retcor --> |
205 <test> | 206 <test> |
206 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/> | 207 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/> |
207 <conditional name="methods"> | 208 <conditional name="methods"> |
208 <param name="method" value="PeakDensity"/> | 209 <param name="method" value="PeakDensity"/> |
209 <param name="bw" value="5"/> | 210 <param name="bw" value="5"/> |
210 <param name="minFraction" value="0.3"/> | 211 <param name="minFraction" value="0.3"/> |
211 <param name="binSize" value="0.01"/> | 212 <param name="binSize" value="0.01"/> |
218 <has_text text="bw: 5" /> | 219 <has_text text="bw: 5" /> |
219 <has_text text="minFraction: 0.3" /> | 220 <has_text text="minFraction: 0.3" /> |
220 <has_text text="binSize: 0.01"/> | 221 <has_text text="binSize: 0.01"/> |
221 <has_text text="maxFeatures: 50" /> | 222 <has_text text="maxFeatures: 50" /> |
222 <has_text text="object with 4 samples" /> | 223 <has_text text="object with 4 samples" /> |
223 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> | 224 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" /> |
224 <has_text text="Mass range: 200.1-600 m/z" /> | 225 <has_text text="Mass range: 200.1-600 m/z" /> |
225 <has_text text="Peaks: 9251 (about 2313 per sample)" /> | 226 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
226 <has_text text="Peak Groups: 8372" /> | 227 <has_text text="Peak Groups: 8209" /> |
227 <has_text text="Sample classes: KO, WT" /> | 228 <has_text text="Sample classes: KO, WT" /> |
228 </assert_stdout> | 229 </assert_stdout> |
229 </test> | 230 </test> |
230 <!-- DISABLE FOR TRAVIS | 231 <!-- DISABLE FOR TRAVIS |
231 Test to test the different methods parameters | 232 Test to test the different methods parameters |
353 --------------------------------------------------- | 354 --------------------------------------------------- |
354 | 355 |
355 Changelog/News | 356 Changelog/News |
356 -------------- | 357 -------------- |
357 | 358 |
358 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS | 359 @HELP_XCMS_NEWVERSION_31200@ |
359 | 360 |
360 **Version 3.6.1+galaxy1 - 22/04/2020** | 361 **Version 3.6.1+galaxy1 - 22/04/2020** |
361 | 362 |
362 - BUGFIX: sample group colours were not displayed in plots. | 363 - BUGFIX: sample group colours were not displayed in plots. |
363 | 364 |