Mercurial > repos > galaxyp > openms_featurefinderidentification
comparison FeatureFinderIdentification.xml @ 13:5471eba33b70 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:07:34 +0000 |
| parents | c1beeebc9db7 |
| children | 5dc928c83939 |
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| 12:8bdf87119680 | 13:5471eba33b70 |
|---|---|
| 156 <expand macro="list_string_san"/> | 156 <expand macro="list_string_san"/> |
| 157 </param> | 157 </param> |
| 158 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> | 158 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> |
| 159 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/> | 159 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/> |
| 160 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/> | 160 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/> |
| 161 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/> | |
| 161 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> | 162 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> |
| 162 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/> | 163 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/> |
| 163 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> | 164 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> |
| 164 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/> | 165 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> |
| 165 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/> | 166 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> |
| 166 </section> | 167 </section> |
| 167 </section> | 168 </section> |
| 168 <expand macro="adv_opts_macro"> | 169 <expand macro="adv_opts_macro"> |
| 169 <param name="candidates_in" argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/> | 170 <param name="candidates_in" argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/> |
| 170 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | 171 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
| 171 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 172 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
| 172 <expand macro="list_string_san"/> | 173 <expand macro="list_string_san"/> |
| 173 </param> | 174 </param> |
| 174 </expand> | 175 </expand> |
| 175 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 176 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
| 176 <option value="lib_out_FLAG">lib_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option> | 177 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option> |
| 177 <option value="chrom_out_FLAG">chrom_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option> | 178 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option> |
| 178 <option value="candidates_out_FLAG">candidates_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option> | 179 <option value="candidates_out_FLAG">candidates_out (Output file: Feature candidates (before filtering and model fitting))</option> |
| 179 <option value="xval_out_FLAG">xval_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option> | 180 <option value="xval_out_FLAG">xval_out (Output file: SVM cross-validation (parameter optimization) results)</option> |
| 180 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 181 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
| 181 </param> | 182 </param> |
| 182 </inputs> | 183 </inputs> |
| 183 <outputs> | 184 <outputs> |
| 184 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> | 185 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
| 203 <expand macro="manutest_FeatureFinderIdentification"/> | 204 <expand macro="manutest_FeatureFinderIdentification"/> |
| 204 </tests> | 205 </tests> |
| 205 <help><![CDATA[Detects features in MS1 data based on peptide identifications. | 206 <help><![CDATA[Detects features in MS1 data based on peptide identifications. |
| 206 | 207 |
| 207 | 208 |
| 208 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderIdentification.html]]></help> | 209 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderIdentification.html]]></help> |
| 209 <expand macro="references"/> | 210 <expand macro="references"/> |
| 210 </tool> | 211 </tool> |