diff macros_test.xml @ 17:abffdfee3021 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"

--- a/macros_test.xml	Fri Nov 06 19:49:28 2020 +0000
+++ b/macros_test.xml	Mon Feb 22 10:46:10 2021 +0000
@@ -127,8 +127,8 @@
   <param name="in" value="IDRipper_2_input.idXML"/>
   <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
   <output_collection name="out_path" count="2">
-    <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
-    <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
+    <element name="IDRipper_2_output_1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
+    <element name="IDRipper_2_output_2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
   </output_collection>
   <output name="ctd_out" ftype="xml">
     <assert_contents>
@@ -266,17 +266,16 @@
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
     <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
     </output_collection>
   </test>
-  
   <!-- test with two inputs (actually the same file .. symlinked) -->
   <test>
     <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
     <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
     <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
+      <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
     </output_collection>
   </test>
 </xml>
@@ -335,6 +334,7 @@
     <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
   </test>
 </xml>
+<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 -->
 <xml name="manutest_PSMFeatureExtractor">
   <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
     <param name="adv_opts_cond|test" value="true"/>
@@ -354,6 +354,13 @@
     <param name="out_type" value="mzid"/>
     <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" 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_cond|test" value="true"/>
+    <param name="in_single" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
+    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
+    <param name="out_type" value="idxml"/>
+    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
+  </test>
 </xml>
 <xml name="manutest_QCCalculator">
   <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->