Mercurial > repos > galaxyp > openms_openswathrtnormalizer
diff OpenSwathRTNormalizer.xml @ 15:0200289da8e1 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 18:19:05 +0000 |
parents | 3a841eba4877 |
children |
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--- a/OpenSwathRTNormalizer.xml Wed Sep 23 14:18:07 2020 +0000 +++ b/OpenSwathRTNormalizer.xml Tue Oct 13 18:19:05 2020 +0000 @@ -93,6 +93,9 @@ <expand macro="list_string_san"/> </param> <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/> + <param name="strict" argument="-algorithm:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""> + <expand macro="list_string_san"/> + </param> <section name="TransitionGroupPicker" title="" help="" expanded="false"> <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/> @@ -209,12 +212,12 @@ <param name="MinBinsFilled" argument="-peptideEstimation:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/> </section> <expand macro="adv_opts_macro"> - <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"> + <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> @@ -231,6 +234,6 @@ <help><![CDATA[This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. -For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathRTNormalizer.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathRTNormalizer.html]]></help> <expand macro="references"/> </tool>