Mercurial > repos > galaxyp > peptideshaker

comparison ident_params.xml @ 61:3ec27b4cee7c draft default tip

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"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
comparison
equal deleted inserted replaced
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>