Mercurial > repos > galaxyp > peptideshaker
comparison ident_params.xml @ 61:3ec27b4cee7c draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
| author | galaxyp |
|---|---|
| date | Thu, 12 Aug 2021 14:06:52 +0000 |
| parents | 943a34df6047 |
| children |
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| 60:a6ff76e057fd | 61:3ec27b4cee7c |
|---|---|
| 523 | 523 |
| 524 ## -- ADVANCED PARAMETERS | 524 ## -- ADVANCED PARAMETERS |
| 525 | 525 |
| 526 ## SPECTRUM ANNOTATION | 526 ## SPECTRUM ANNOTATION |
| 527 -annotation_level $advanced_options.spectrum_annotation_options.annotation_level | 527 -annotation_level $advanced_options.spectrum_annotation_options.annotation_level |
| 528 | |
| 529 ## if the user modifies fragment_tol but he does not modify annotation_mz_tolerance, | |
| 530 ## we must overwrite default annotation_mz_tolerance value with fragment_tol value | |
| 531 | |
| 532 #if not ($spectrum_matching_options.fragment_tol != 0.5 and $advanced_options.spectrum_annotation_options.annotation_mz_tolerance == 0.5) | |
| 528 -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance | 533 -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance |
| 534 #end if | |
| 529 -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution | 535 -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution |
| 530 ## TODO: There are still many options from the GUI to be incorporated to the CLI | 536 ## TODO: There are still many options from the GUI to be incorporated to the CLI |
| 531 | 537 |
| 532 | 538 |
| 533 ## SEQUENCE MATCHING | 539 ## SEQUENCE MATCHING |
| 1201 <option value="8">unspecific N-term</option> | 1207 <option value="8">unspecific N-term</option> |
| 1202 <option value="9">unspecific C-term</option> | 1208 <option value="9">unspecific C-term</option> |
| 1203 </param> | 1209 </param> |
| 1204 <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> | 1210 <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> |
| 1205 <option value="0">off</option> | 1211 <option value="0">off</option> |
| 1206 <option value="1" selected="True">0,+1</option> | 1212 <option value="1">0,+1</option> |
| 1207 <option value="2">0,+1,+2</option> | 1213 <option value="2">0,+1,+2</option> |
| 1208 <option value="3">0,+1,+2,+3</option> | 1214 <option value="3" selected="True">0,+1,+2,+3</option> |
| 1209 <option value="4">-8,-4,0,+4,+8</option> | 1215 <option value="4">-8,-4,0,+4,+8</option> |
| 1210 </param> | 1216 </param> |
| 1211 <param name="comet_min_prec_mass" type="float" value="600.0" | 1217 <param name="comet_min_prec_mass" type="float" value="600.0" |
| 1212 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> | 1218 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> |
| 1213 <param name="comet_max_prec_mass" type="float" value="5000.0" | 1219 <param name="comet_max_prec_mass" type="float" value="5000.0" |
| 1235 <param name="comet_theoretical_fragment_ions" type="select" | 1241 <param name="comet_theoretical_fragment_ions" type="select" |
| 1236 label="Comet: Correlation Score type" help="Specifies how theoretical fragment ion peaks are represented (on the sum in the bin alone or using flanking bins too)"> | 1242 label="Comet: Correlation Score type" help="Specifies how theoretical fragment ion peaks are represented (on the sum in the bin alone or using flanking bins too)"> |
| 1237 <option value="0" selected="True">Summed intensities + flanking</option> | 1243 <option value="0" selected="True">Summed intensities + flanking</option> |
| 1238 <option value="1">Summed intensities</option> | 1244 <option value="1">Summed intensities</option> |
| 1239 </param> | 1245 </param> |
| 1240 <param name="comet_frag_bin_offset" type="float" value="0.01" | 1246 <param name="comet_frag_bin_offset" type="float" value="0" |
| 1241 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> | 1247 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> |
| 1242 </when> | 1248 </when> |
| 1243 </conditional> | 1249 </conditional> |
| 1244 <!-- Output Related parameters --> | 1250 <!-- Output Related parameters --> |
| 1245 <conditional name="comet_output"> | 1251 <conditional name="comet_output"> |
| 1704 | 1710 |
| 1705 <section name="spectrum_annotation_options" expanded="false" title="Spectrum Annotation Options"> | 1711 <section name="spectrum_annotation_options" expanded="false" title="Spectrum Annotation Options"> |
| 1706 <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float"> | 1712 <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float"> |
| 1707 <validator type="in_range" min="0" max="1" /> | 1713 <validator type="in_range" min="0" max="1" /> |
| 1708 </param> | 1714 </param> |
| 1709 <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="10" type="float" /> | 1715 <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="0.5" type="float" /> |
| 1710 <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/> | 1716 <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/> |
| 1711 </section> | 1717 </section> |
| 1712 | 1718 |
| 1713 <!-- SEQUENCE MATCHING --> | 1719 <!-- SEQUENCE MATCHING --> |
| 1714 | 1720 |
| 1849 <option value="yes" selected="True">Yes</option> | 1855 <option value="yes" selected="True">Yes</option> |
| 1850 <option value="no" >No</option> | 1856 <option value="no" >No</option> |
| 1851 </param> | 1857 </param> |
| 1852 <when value="no" /> | 1858 <when value="no" /> |
| 1853 <when value="yes"> | 1859 <when value="yes"> |
| 1854 <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag"> | 1860 <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag"> |
| 1855 </param> | 1861 </param> |
| 1856 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix"> | 1862 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix"> |
| 1857 <option value="0">Prefix</option> | 1863 <option value="0">Prefix</option> |
| 1858 <option value="1" selected="True">Suffix</option> | 1864 <option value="1" selected="True">Suffix</option> |
| 1859 </param> | 1865 </param> |