Mercurial > repos > galaxyp > openms_featurefindermetaboident

comparison FeatureFinderMetaboIdent.xml @ 2:7e29bf457263 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 19:55:30 +0000
parents 539b683e9752
children ae20e8a6d309
comparison
equal deleted inserted replaced
1:59c8b1a9cf86 2:7e29bf457263
109 <expand macro="list_string_san"/> 109 <expand macro="list_string_san"/>
110 </param> 110 </param>
111 <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"/> 111 <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"/>
112 <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=""/> 112 <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=""/>
113 <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=""/> 113 <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=""/>
114 <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=""/>
114 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> 115 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
115 <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=""/> 116 <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=""/>
116 <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=""/> 117 <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=""/>
117 <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=""/> 118 <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')"/>
118 <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=""/> 119 <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')"/>
119 </section> 120 </section>
120 </section> 121 </section>
121 <expand macro="adv_opts_macro"> 122 <expand macro="adv_opts_macro">
122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 123 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
123 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 124 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
124 <expand macro="list_string_san"/> 125 <expand macro="list_string_san"/>
125 </param> 126 </param>
126 </expand> 127 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
128 <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> 129 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
129 <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> 130 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
130 <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> 131 <option value="candidates_out_FLAG">candidates_out (Output file: Feature candidates (before filtering and model fitting))</option>
131 <option value="trafo_out_FLAG">trafo_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option> 132 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
132 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
133 </param> 134 </param>
134 </inputs> 135 </inputs>
135 <outputs> 136 <outputs>
136 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 137 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
155 <expand macro="manutest_FeatureFinderMetaboIdent"/> 156 <expand macro="manutest_FeatureFinderMetaboIdent"/>
156 </tests> 157 </tests>
157 <help><![CDATA[Detects features in MS1 data based on metabolite identifications. 158 <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
158 159
159 160
160 For more information, visit http://www.openms.de/documentation/UTILS_FeatureFinderMetaboIdent.html]]></help> 161 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help>
161 <expand macro="references"/> 162 <expand macro="references"/>
162 </tool> 163 </tool>