--- a/SiriusAdapter.xml	Fri Nov 06 18:45:32 2020 +0000
+++ b/SiriusAdapter.xml	Mon Dec 14 08:27:40 2020 +0000
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05">
   <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
   <macros>
     <token name="@EXECUTABLE@">SiriusAdapter</token>
@@ -75,14 +75,11 @@
 #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, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "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)"/>
     <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
-    <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
-      <expand macro="list_string_san"/>
-    </param>
     <section name="preprocessing" title="Preprocessing" help="" expanded="false">
       <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/>
       <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>