Mercurial > repos > galaxyp > openms_isobaricanalyzer
comparison IsobaricAnalyzer.xml @ 4:bec6abb425bf draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
| author | galaxyp |
|---|---|
| date | Fri, 14 Jul 2017 18:53:23 -0400 |
| parents | ef60d1479807 |
| children | 093d79941931 |
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| 3:eb2f29cfe471 | 4:bec6abb425bf |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> |
| 3 <!--Proposed Tool Section: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
| 4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.1.0"> | 4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0"> |
| 5 <description>Calculates isobaric quantitative values for peptides</description> | 5 <description>Calculates isobaric quantitative values for peptides</description> |
| 6 <macros> | 6 <macros> |
| 7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token> | 7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token> |
| 8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
| 9 </macros> | 9 </macros> |
| 239 <option value="itraq8plex">itraq8plex</option> | 239 <option value="itraq8plex">itraq8plex</option> |
| 240 <option value="tmt10plex">tmt10plex</option> | 240 <option value="tmt10plex">tmt10plex</option> |
| 241 <option value="tmt6plex">tmt6plex</option> | 241 <option value="tmt6plex">tmt6plex</option> |
| 242 </param> | 242 </param> |
| 243 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> | 243 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> |
| 244 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)"> | 244 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)"> |
| 245 <sanitizer> | 245 <sanitizer> |
| 246 <valid initial="string.printable"> | 246 <valid initial="string.printable"> |
| 247 <remove value="'"/> | 247 <remove value="'"/> |
| 248 <remove value="""/> | 248 <remove value="""/> |
| 249 </valid> | 249 </valid> |
| 262 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> | 262 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> |
| 263 <option value="Photodissociation">Photodissociation</option> | 263 <option value="Photodissociation">Photodissociation</option> |
| 264 <option value="Electron transfer dissociation">Electron transfer dissociation</option> | 264 <option value="Electron transfer dissociation">Electron transfer dissociation</option> |
| 265 <option value=""></option> | 265 <option value=""></option> |
| 266 </param> | 266 </param> |
| 267 <param name="param_extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/> | 267 <param name="param_extraction_reporter_mass_shift" type="float" min="0.0001" max="0.5" optional="True" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help="(-reporter_mass_shift) "/> |
| 268 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> | 268 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> |
| 269 <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) "> | 269 <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) "> |
| 270 <option value="true" selected="true">true</option> | 270 <option value="true" selected="true">true</option> |
| 271 <option value="false">false</option> | 271 <option value="false">false</option> |
| 272 </param> | 272 </param> |