--- a/MetaboliteAdductDecharger.xml	Thu Sep 24 12:23:02 2020 +0000
+++ b/MetaboliteAdductDecharger.xml	Tue Oct 13 20:39:58 2020 +0000
@@ -18,7 +18,9 @@
 ## Preprocessing
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out_cm &&
+#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_cm &&
+#end if
 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_fm &&
 #end if
@@ -34,8 +36,10 @@
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out_cm
-'out_cm/output.${gxy2omsext("consensusxml")}'
+#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_cm
+  'out_cm/output.${gxy2omsext("consensusxml")}'
+#end if
 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_fm
   'out_fm/output.${gxy2omsext("featurexml")}'
@@ -49,7 +53,9 @@
 #end if
 
 ## Postprocessing
-&& mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
+#if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
+#end if
 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
 #end if
@@ -105,25 +111,31 @@
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <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="out_fm_FLAG">out_fm (Amount of debug information given during processing)</option>
-      <option value="outpairs_FLAG">outpairs (Amount of debug information given during processing)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_cm_FLAG">out_cm (output consensus map)</option>
+      <option value="out_fm_FLAG">out_fm (output feature map)</option>
+      <option value="outpairs_FLAG">outpairs (output file)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
-    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"/>
+    <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
       <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
     <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml">
       <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -135,6 +147,6 @@
   <help><![CDATA[Decharges and merges different feature charge variants of the same metabolite.
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_MetaboliteAdductDecharger.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaboliteAdductDecharger.html]]></help>
   <expand macro="references"/>
 </tool>