Mercurial > repos > galaxyp > openms_nucleicacidsearchengine
diff NucleicAcidSearchEngine.xml @ 2:00b91aaec050 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
---|---|
date | Tue, 13 Oct 2020 19:49:38 +0000 |
parents | fe6eddc2e756 |
children | 92864c71ac6a |
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--- a/NucleicAcidSearchEngine.xml Thu Sep 24 09:00:07 2020 +0000 +++ b/NucleicAcidSearchEngine.xml Tue Oct 13 19:49:38 2020 +0000 @@ -363,16 +363,16 @@ </section> <expand macro="adv_opts_macro"> <param name="decharge_ms2" argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> <expand macro="list_string_san"/> </param> </expand> - <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> - <option value="id_out_FLAG">id_out (Do not score hits to decoy sequences and remove them when filtering)</option> - <option value="lfq_out_FLAG">lfq_out (Do not score hits to decoy sequences and remove them when filtering)</option> - <option value="theo_ms2_out_FLAG">theo_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option> - <option value="exp_ms2_out_FLAG">exp_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option> + <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> + <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option> + <option value="lfq_out_FLAG">lfq_out (Output file: Targets for label-free quantification using FeatureFinderMetaboIdent ('id' input))</option> + <option value="theo_ms2_out_FLAG">theo_ms2_out (Output file: theoretical MS2 spectra for precursor mass matches)</option> + <option value="exp_ms2_out_FLAG">exp_ms2_out (Output file: experimental MS2 spectra for precursor mass matches)</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> @@ -401,6 +401,6 @@ <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra. -For more information, visit http://www.openms.de/documentation/UTILS_NucleicAcidSearchEngine.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NucleicAcidSearchEngine.html]]></help> <expand macro="references"/> </tool>