diff OpenSwathRTNormalizer.xml @ 15:0200289da8e1 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 18:19:05 +0000
parents 3a841eba4877
children
line wrap: on
line diff
--- 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>