cleanup

tools/openms/PSMFeatureExtractor.xml

@@ -172,33 +172,6 @@ ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identi
         <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
       </assert_stdout>
     </test>
-    <test expect_num_outputs="1">
-      <!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-      <param name="adv_opts|test" value="true"/>
-      <param name="adv_opts|skip_db_check" value="true"/>
-      <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-      <param name="multiple_search_engines" value="true"/>
-      <param name="out_type" value="idxml"/>
-      <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-    </test>
-    <test expect_num_outputs="1">
-      <!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-      <param name="adv_opts|test" value="true"/>
-      <param name="adv_opts|skip_db_check" value="true"/>
-      <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-      <param name="multiple_search_engines" value="true"/>
-      <param name="out_type" value="mzid"/>
-      <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-    </test>
-    <!-- test for the batch conditional crated for data parameters with multiple="true" -->
-    <test expect_num_outputs="1">
-      <!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-      <param name="adv_opts|test" value="true"/>
-      <param name="in_select" value="yes"/>
-      <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-      <param name="out_type" value="idxml"/>
-      <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
-    </test>
   </tests>
   <help><![CDATA[Computes extra features for each input PSM.
 

tools/openms/SeedListGenerator.xml

@@ -37,7 +37,7 @@ out_prefix/
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
     <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>

tools/openms/aux/hardcoded_params.json

@@ -191,7 +191,6 @@
 	"#": "IDFileConverter remove xml",
 	"#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
     "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
-	"#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. ",
 	"in": [{
 		"CTD:restrictions": "oms,idXML,mzid,fasta,pepXML,protXML,mascotXML,omssaXML,psms,tsv,xquest.xml",
 		"tools": ["IDFileConverter"]
@@ -201,9 +200,6 @@
 	}, {
 		"CTD:restrictions": "idXML,mzid,xquest.xml",
 		"tools": ["XFDR"]
-	}, {
-		"CTD:restrictions": "mzML,idXML,featureXML",
-		"tools": ["SeedListGenerator"]
 	}],
 
 	"#": "IDMapper has in and spectra:in params, in is used in out as format_source",