Mercurial > repos > galaxyp > openms_openswathdecoygenerator

diff OpenSwathDecoyGenerator.xml @ 11:3769d3a7e9ba 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 20:05:47 +0000
parents 1814187218fe
children 496cf619e311
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--- a/OpenSwathDecoyGenerator.xml	Thu Sep 24 12:35:13 2020 +0000
+++ b/OpenSwathDecoyGenerator.xml	Tue Oct 13 20:05:47 2020 +0000
@@ -48,7 +48,7 @@
       <option value="tsv">tabular (tsv)</option>
       <expand macro="list_string_san"/>
     </param>
-    <param name="method" argument="-method" display="radio" type="select" optional="false" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="">
+    <param name="method" argument="-method" display="radio" type="select" optional="false" label="Decoy generation method" help="">
       <option value="shuffle" selected="true">shuffle</option>
       <option value="pseudo-reverse">pseudo-reverse</option>
       <option value="reverse">reverse</option>
@@ -76,12 +76,12 @@
       <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
       <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
       <param name="separate" argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" 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">
+    <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>
@@ -104,6 +104,6 @@
   <help><![CDATA[Generates decoys according to different models for a specific TraML
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathDecoyGenerator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathDecoyGenerator.html]]></help>
   <expand macro="references"/>
 </tool>