Mercurial > repos > galaxyp > openms_idmassaccuracy

comparison IDMassAccuracy.xml @ 13:31bc4129f589 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 20:32:01 +0000
parents 65be0674bb70
children 585f8235da7e
comparison
equal deleted inserted replaced
12:f918cb7aefd5 13:31bc4129f589
89 <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/> 89 <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
90 <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/> 90 <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
91 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/> 91 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
92 <expand macro="adv_opts_macro"> 92 <expand macro="adv_opts_macro">
93 <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/> 93 <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
96 <expand macro="list_string_san"/> 96 <expand macro="list_string_san"/>
97 </param> 97 </param>
98 </expand> 98 </expand>
99 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
100 <option value="out_precursor_FLAG">out_precursor (Enables the test mode (needed for internal use only))</option> 100 <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option>
101 <option value="out_fragment_FLAG">out_fragment (Enables the test mode (needed for internal use only))</option> 101 <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option>
102 <option value="out_precursor_fit_FLAG">out_precursor_fit (Enables the test mode (needed for internal use only))</option> 102 <option value="out_precursor_fit_FLAG">out_precursor_fit (Gaussian fit to the histogram of mass deviations from the precursors)</option>
103 <option value="out_fragment_fit_FLAG">out_fragment_fit (Enables the test mode (needed for internal use only))</option> 103 <option value="out_fragment_fit_FLAG">out_fragment_fit (Gaussian fit to the histogram of mass deviations from the fragments)</option>
104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
105 </param> 105 </param>
106 </inputs> 106 </inputs>
107 <outputs> 107 <outputs>
108 <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular"> 108 <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">
129 <expand macro="manutest_IDMassAccuracy"/> 129 <expand macro="manutest_IDMassAccuracy"/>
130 </tests> 130 </tests>
131 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs. 131 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
132 132
133 133
134 For more information, visit http://www.openms.de/documentation/UTILS_IDMassAccuracy.html]]></help> 134 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDMassAccuracy.html]]></help>
135 <expand macro="references"/> 135 <expand macro="references"/>
136 </tool> 136 </tool>