Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 33:f5d51091cf84 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:22:36 +0000
parents b02d1992a43a
children
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32:b02d1992a43a 33:f5d51091cf84
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" />