Mercurial > repos > lecorguille > xcms_group

comparison abims_xcms_group.xml @ 27:d45a786cbc40 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 12:06:33 +0000
parents 0d05d0458376
children 2b676d5eb848
comparison
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26:0d05d0458376 27:d45a786cbc40
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