Mercurial > repos > galaxyp > openms_openswathassaygenerator

comparison OpenSwathAssayGenerator.xml @ 11:a41cd777ced9 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 20:09:00 +0000
parents 5848492bfc5a
children de7a553552a6
comparison
equal deleted inserted replaced
10:df72ca515420 11:a41cd777ced9
87 <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/> 87 <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
88 <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/> 88 <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
89 <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/> 89 <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
90 <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/> 90 <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
91 <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/> 91 <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
92 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 92 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
93 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 93 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
94 <expand macro="list_string_san"/> 94 <expand macro="list_string_san"/>
95 </param> 95 </param>
96 </expand> 96 </expand>
97 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 97 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
99 </param> 99 </param>
100 </inputs> 100 </inputs>
101 <outputs> 101 <outputs>
102 <data name="out" label="${tool.name} on ${on_string}: out"> 102 <data name="out" label="${tool.name} on ${on_string}: out">
115 <expand macro="manutest_OpenSwathAssayGenerator"/> 115 <expand macro="manutest_OpenSwathAssayGenerator"/>
116 </tests> 116 </tests>
117 <help><![CDATA[Generates assays according to different models for a specific TraML 117 <help><![CDATA[Generates assays according to different models for a specific TraML
118 118
119 119
120 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAssayGenerator.html]]></help> 120 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
121 <expand macro="references"/> 121 <expand macro="references"/>
122 </tool> 122 </tool>