Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 6:465623d2f6fa draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
| author | lecorguille |
|---|---|
| date | Mon, 04 Jul 2016 08:46:35 -0400 |
| parents | cd351af95d14 |
| children | cce30b3398e0 |
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| 5:cd351af95d14 | 6:465623d2f6fa |
|---|---|
| 16 | 16 |
| 17 xsetRdataOutput $xsetRData | 17 xsetRdataOutput $xsetRData |
| 18 | 18 |
| 19 method $method | 19 method $method |
| 20 | 20 |
| 21 #if $zip_file: | 21 @COMMAND_ZIPFILE_LOAD@ |
| 22 zipfile $zip_file | 22 |
| 23 #end if | |
| 24 @COMMAND_LOG_EXIT@ | 23 @COMMAND_LOG_EXIT@ |
| 25 | 24 |
| 26 ]]></command> | 25 ]]></command> |
| 27 | 26 |
| 28 <inputs> | 27 <inputs> |
| 29 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> | 28 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> |
| 30 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> | 29 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> |
| 31 <option value="chrom" selected="true">chrom</option> | 30 <option value="chrom" selected="true">chrom</option> |
| 32 <option value="MSW" >MSW</option> | 31 <option value="MSW" >MSW</option> |
| 33 </param> | 32 </param> |
| 34 <!-- To pass planemo test --> | 33 |
| 35 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> | 34 <expand macro="zipfile_load"/> |
| 35 | |
| 36 </inputs> | 36 </inputs> |
| 37 | 37 |
| 38 <outputs> | 38 <outputs> |
| 39 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> | 39 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> |
| 40 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> | 40 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
| 57 </output> | 57 </output> |
| 58 </test>--> | 58 </test>--> |
| 59 <test> | 59 <test> |
| 60 <param name="image" value="faahKO.xset.group.retcor.group.RData"/> | 60 <param name="image" value="faahKO.xset.group.retcor.group.RData"/> |
| 61 <param name="method" value="chrom"/> | 61 <param name="method" value="chrom"/> |
| 62 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> | 62 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> |
| 63 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> | |
| 63 <output name="log"> | 64 <output name="log"> |
| 64 <assert_contents> | 65 <assert_contents> |
| 65 <has_text text="object with 4 samples" /> | 66 <has_text text="object with 4 samples" /> |
| 66 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> | 67 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> |
| 67 <has_text text="Mass range: 200.1-600 m/z" /> | 68 <has_text text="Mass range: 200.1-600 m/z" /> |