Mercurial > repos > galaxyp > openms_featurefindermetabo

comparison FeatureFinderMetabo.xml @ 13:00080bb4299e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:38:53 +0000
parents 21dc135961b5
children 2451315543f9
comparison
equal deleted inserted replaced
12:ede71c074e9a 13:00080bb4299e
86 <option value="off">off</option> 86 <option value="off">off</option>
87 <option value="fixed" selected="true">fixed</option> 87 <option value="fixed" selected="true">fixed</option>
88 <option value="auto">auto</option> 88 <option value="auto">auto</option>
89 <expand macro="list_string_san"/> 89 <expand macro="list_string_san"/>
90 </param> 90 </param>
91 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 91 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
92 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 92 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
93 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/> 93 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
94 </section> 94 </section>
95 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false"> 95 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
96 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/> 96 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
115 <expand macro="list_string_san"/> 115 <expand macro="list_string_san"/>
116 </param> 116 </param>
117 </section> 117 </section>
118 </section> 118 </section>
119 <expand macro="adv_opts_macro"> 119 <expand macro="adv_opts_macro">
120 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 120 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
121 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 121 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
122 <expand macro="list_string_san"/> 122 <expand macro="list_string_san"/>
123 </param> 123 </param>
124 </expand> 124 </expand>
125 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
126 <option value="out_chrom_FLAG">out_chrom (Elements assumes to be present in the sample (this influences isotope detection))</option> 126 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option>
127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
128 </param> 128 </param>
129 </inputs> 129 </inputs>
130 <outputs> 130 <outputs>
131 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 131 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
141 <expand macro="manutest_FeatureFinderMetabo"/> 141 <expand macro="manutest_FeatureFinderMetabo"/>
142 </tests> 142 </tests>
143 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 143 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
144 144
145 145
146 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMetabo.html]]></help> 146 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMetabo.html]]></help>
147 <expand macro="references"/> 147 <expand macro="references"/>
148 </tool> 148 </tool>