Mercurial > repos > lecorguille > xcms_retcor
comparison abims_xcms_retcor.xml @ 4:ac93ed26e4e1 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
| author | lecorguille |
|---|---|
| date | Mon, 04 Jul 2016 08:46:17 -0400 |
| parents | 3b44991a8e05 |
| children | 123824c7eaa8 |
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| 3:3b44991a8e05 | 4:ac93ed26e4e1 |
|---|---|
| 30 span $methods.options.span | 30 span $methods.options.span |
| 31 family $methods.options.family | 31 family $methods.options.family |
| 32 plottype $methods.options.plottype | 32 plottype $methods.options.plottype |
| 33 #end if | 33 #end if |
| 34 #end if | 34 #end if |
| 35 #if $zip_file: | 35 |
| 36 zipfile $zip_file | 36 @COMMAND_ZIPFILE_LOAD@ |
| 37 #end if | 37 |
| 38 @COMMAND_LOG_EXIT@ | 38 @COMMAND_LOG_EXIT@ |
| 39 ]]></command> | 39 ]]></command> |
| 40 | 40 |
| 41 <inputs> | 41 <inputs> |
| 42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> | 42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> |
| 79 <when value="hide"> | 79 <when value="hide"> |
| 80 </when> | 80 </when> |
| 81 </conditional> | 81 </conditional> |
| 82 </when> | 82 </when> |
| 83 </conditional> | 83 </conditional> |
| 84 <!-- To pass planemo test --> | 84 |
| 85 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> | 85 <expand macro="zipfile_load"/> |
| 86 | |
| 86 </inputs> | 87 </inputs> |
| 87 | 88 |
| 88 <outputs> | 89 <outputs> |
| 89 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> | 90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> |
| 90 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> | 91 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> |
| 107 <param name="methods|missing" value="1"/> | 108 <param name="methods|missing" value="1"/> |
| 108 <param name="methods|options|option" value="show"/> | 109 <param name="methods|options|option" value="show"/> |
| 109 <param name="methods|options|span" value="0.2"/> | 110 <param name="methods|options|span" value="0.2"/> |
| 110 <param name="methods|options|family" value="gaussian"/> | 111 <param name="methods|options|family" value="gaussian"/> |
| 111 <param name="methods|options|plottype" value="deviation"/> | 112 <param name="methods|options|plottype" value="deviation"/> |
| 112 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> | 113 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> |
| 114 <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> | |
| 113 <output name="log"> | 115 <output name="log"> |
| 114 <assert_contents> | 116 <assert_contents> |
| 115 <has_text text="object with 4 samples" /> | 117 <has_text text="object with 4 samples" /> |
| 116 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> | 118 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> |
| 117 <has_text text="Mass range: 50.0021-999.9863 m/z" /> | 119 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
| 129 <param name="methods|missing" value="1"/> | 131 <param name="methods|missing" value="1"/> |
| 130 <param name="methods|options|option" value="show"/> | 132 <param name="methods|options|option" value="show"/> |
| 131 <param name="methods|options|span" value="0.2"/> | 133 <param name="methods|options|span" value="0.2"/> |
| 132 <param name="methods|options|family" value="gaussian"/> | 134 <param name="methods|options|family" value="gaussian"/> |
| 133 <param name="methods|options|plottype" value="deviation"/> | 135 <param name="methods|options|plottype" value="deviation"/> |
| 134 <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> | 136 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> |
| 137 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> | |
| 135 <output name="log"> | 138 <output name="log"> |
| 136 <assert_contents> | 139 <assert_contents> |
| 137 <has_text text="object with 4 samples" /> | 140 <has_text text="object with 4 samples" /> |
| 138 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> | 141 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> |
| 139 <has_text text="Mass range: 200.1-600 m/z" /> | 142 <has_text text="Mass range: 200.1-600 m/z" /> |