Mercurial > repos > lecorguille > xcms_xcmsset
comparison abims_xcms_xcmsSet.xml @ 33:f5d51091cf84 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:22:36 +0000 |
parents | b02d1992a43a |
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32:b02d1992a43a | 33:f5d51091cf84 |
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1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> | 1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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> |
185 </inputs> | 185 </inputs> |
186 | 186 |
187 <outputs> | 187 <outputs> |
188 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" /> | 188 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" /> |
189 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" /> | 189 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" /> |
190 <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > | 190 <data name="peaklist_out" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > |
191 <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter> | 191 <filter>methods['method'] in ['CentWave', 'MatchedFilter'] and (methods['CentWaveAdv']['peaklist'])</filter> |
192 </data> | |
193 <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > | |
194 <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter> | |
195 </data> | 192 </data> |
196 </outputs> | 193 </outputs> |
197 | 194 |
198 <tests> | 195 <tests> |
199 | 196 |
225 <has_text text="Peaks: 1311 (about 328 per sample)" /> | 222 <has_text text="Peaks: 1311 (about 328 per sample)" /> |
226 <has_text text="Peak Groups: 0" /> | 223 <has_text text="Peak Groups: 0" /> |
227 <has_text text="Sample classes: KO, WT" /> | 224 <has_text text="Sample classes: KO, WT" /> |
228 </assert_stdout> | 225 </assert_stdout> |
229 </test>--> | 226 </test>--> |
230 <test> | 227 <test expect_num_outputs="2"> |
231 <param name="image" value="ko15-raw.RData" ftype="rdata" /> | 228 <param name="image" value="ko15-raw.RData" ftype="rdata" /> |
232 <conditional name="methods"> | 229 <conditional name="methods"> |
233 <param name="method" value="CentWave" /> | 230 <param name="method" value="CentWave" /> |
234 <param name="ppm" value="25" /> | 231 <param name="ppm" value="25" /> |
235 <param name="peakwidth" value="20,50" /> | 232 <param name="peakwidth" value="20,50" /> |