--- a/SiriusAdapter.xml	Thu Sep 24 12:07:35 2020 +0000
+++ b/SiriusAdapter.xml	Tue Oct 13 20:11:33 2020 +0000
@@ -75,7 +75,7 @@
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
   </configfiles>
   <inputs>
     <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
@@ -139,7 +139,6 @@
       <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
       <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
       <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
-      <param name="cores" argument="-sirius:cores" type="integer" optional="true" min="1" value="1" label="The number of cores SIRIUS is allowed to use on the system" help=""/>
       <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
       <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
       <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
@@ -147,15 +146,15 @@
     </section>
     <expand macro="adv_opts_macro">
       <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/>
-      <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_sirius_FLAG">out_sirius (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
-      <option value="out_fingerid_FLAG">out_fingerid (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
-      <option value="out_ms_FLAG">out_ms (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_sirius_FLAG">out_sirius (MzTab Output file for SiriusAdapter results)</option>
+      <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
+      <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -183,6 +182,6 @@
   <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_SiriusAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SiriusAdapter.html]]></help>
   <expand macro="references"/>
 </tool>