Mercurial > repos > galaxyp > openms_openswathanalyzer

diff OpenSwathAnalyzer.xml @ 11:7ca917175b23 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 19:43:44 +0000
parents bc57c90ba60f
children 08488066d588
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--- a/OpenSwathAnalyzer.xml	Thu Sep 24 12:33:57 2020 +0000
+++ b/OpenSwathAnalyzer.xml	Tue Oct 13 19:43:44 2020 +0000
@@ -98,6 +98,9 @@
         <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=""/>
@@ -207,12 +210,12 @@
       </section>
     </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>
@@ -229,6 +232,6 @@
   <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAnalyzer.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
   <expand macro="references"/>
 </tool>