remove some hardcoding for prefix output param

tools/openms/OpenSwathFileSplitter.xml

@@ -15,7 +15,9 @@
 ## Preprocessing
 mkdir in &&
 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir outputDirectory &&
+#if "outputDirectory_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir adv_opts.outputDirectory &&
+#end if
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_qc &&
 #end if
@@ -28,8 +30,10 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
 @EXECUTABLE@ -ini @[email protected]
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--outputDirectory
-outputDirectory/
+#if "outputDirectory_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -outputDirectory
+  adv_opts.outputDirectory/
+#end if
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_qc
   'out_qc/output.${gxy2omsext("json")}'
@@ -58,17 +62,22 @@ outputDirectory/
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="outputDirectory_FLAG">outputDirectory (Output file prefix)</option>
       <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
-    <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
-      <discover_datasets directory="outputDirectory" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+    <collection type="list" name="adv_opts_outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
+      <discover_datasets directory="adv_opts_outputDirectory" recurse="true" format="txt" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+      <filter>OPTIONAL_OUTPUTS is not None and "outputDirectory_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
     <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
       <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
+    <data name="stdout" format="txt" label="${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>

tools/openms/aux/hardcoded_params.json

@@ -207,16 +207,6 @@
 		"tools": ["IDMapper"]
 	}],
 
-	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/5912",
-	"#": "output-prefix",
-	"outputDirectory": [{
-		"CTD:type": "output-prefix", 
-		"CTD:advanced": false,
-		"CTD:required": true,
-		"CTD:restrictions": "mzml",
-		"tools": ["OpenSwathFileSplitter"]
-	}],
-
 	"#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
 	"output_files": [{
 		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",