diff PrecursorIonSelector.xml @ 11:fa7a58de2977 draft

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

--- a/PrecursorIonSelector.xml	Thu Sep 24 09:01:49 2020 +0000
+++ b/PrecursorIonSelector.xml	Tue Oct 13 19:47:24 2020 +0000
@@ -103,7 +103,7 @@
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
   </configfiles>
   <inputs>
     <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
@@ -198,15 +198,15 @@
         <option value="COINOR">COINOR</option>
         <expand macro="list_string_san"/>
       </param>
-      <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="false">
-      <option value="out_FLAG">out (std of the gauss curve)</option>
-      <option value="next_feat_FLAG">next_feat (std of the gauss curve)</option>
-      <option value="sim_results_FLAG">sim_results (std of the gauss curve)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_FLAG">out (modified feature map)</option>
+      <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>
+      <option value="sim_results_FLAG">sim_results (File containing the results of the simulation run)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -234,6 +234,6 @@
   <help><![CDATA[PrecursorIonSelector
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_PrecursorIonSelector.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PrecursorIonSelector.html]]></help>
   <expand macro="references"/>
 </tool>