diff NucleicAcidSearchEngine.xml @ 2:00b91aaec050 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- 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>