comparison macros_test.xml @ 13:31bc4129f589 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

12:f918cb7aefd5

    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
  </test>
</xml>
<xml name="manutest_MetaboliteAdductDecharger">
  <test expect_num_outputs="3"><!-- same input as used by Decharger -->
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="featurexml" value="Decharger_input.featureXML"/>
    <output name="out_cm" ftype="consensusxml" value="MetaboliteAdductDecharger_cm.consensusXML" compare="sim_size"/>
    <param name="OPTIONAL_OUTPUTS" value="out_fm_FLAG,outpairs_FLAG"/>
    <output name="out_fm" ftype="featurexml" value="MetaboliteAdductDecharger_fm.featureXML" compare="sim_size"/>
    <output name="outpairs" ftype="consensusxml" value="MetaboliteAdductDecharger_pairs.consensusXML" compare="sim_size"/>
  </test>
</xml>
<xml name="manutest_MetaboliteSpectralMatcher">
    <!-- https://github.com/OpenMS/OpenMS/issues/2078 
        https://github.com/OpenMS/OpenMS/pull/4468-->
    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="mzml" value="spectra.mzML"/>

    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
  </output_collection>
</test>
</xml>
<xml name="manutest_OpenSwathDIAPreScoring">
  <!-- TODO data from a test that included all the needed test files 
       currently unusable https://github.com/OpenMS/OpenMS/pull/4443 -->
  <!-- data from a test that included all the needed test files -->
<!--  <test>-->
<!--    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>-->
<!--    <param name="swath_files" value="OpenSwathWorkflow_10.chrom.mzML.tmp"/> or OpenSwathAnalyzer_2_swathfile.mzML-->
<!--    <output name="out" ftype="tabular" value="OpenSwathDIAPreScoring_2.tmp"/>-->
<!--  </test>-->
</xml>
<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
<xml name="manutest_OpenSwathFileSplitter">
<test expect_num_outputs="3">
  <conditional name="adv_opts_cond">
    <param name="adv_opts_selector" value="advanced"/>
    <param name="force" value="false"/>
    <param name="test" value="true"/>
  </conditional>
  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
  <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
  <output_collection name="outputDirectory" count="6">
    <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
    <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
  </output_collection>
  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
  <output name="ctd_out" ftype="xml">
    <assert_contents>
      <is_valid_xml/>
    </assert_contents>
  </output>
</test>
</xml>
<xml name="manutest_OpenSwathRewriteToFeatureXML">
  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
    <param name="adv_opts_cond|test" 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="adv_opts_cond|adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|skip_db_check" value="true"/>
    <param name="out_type" value="idxml"/>
    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="100"/>
  </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" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
    <param name="multiple_search_engines" value="true"/>
    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|skip_db_check" value="true"/>
    <param name="out_type" value="mzid"/>
    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="100" lines_diff="4"/>
  </test>
</xml>
<xml name="manutest_QCCalculator">
  <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
    <param name="adv_opts_selector" value="advanced"/>

    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
  </test>
</xml>
<xml name="manutest_RTEvaluation">
  <!-- just chosen an arbitrary input and autgenerated output-->
  <!-- https://github.com/OpenMS/OpenMS/pull/4429 -->
  <test expect_num_outputs="1">
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
    <output name="out" ftype="csv" value="RTEvaluation.tsv"/>
  </test>
</xml>
<xml name="manutest_SemanticValidator">
  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
    <param name="adv_opts_selector" value="advanced"/>

    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
    </output>
  </test>
</xml>
<xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/></macros>

13:31bc4129f589

    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
  </test>
</xml>
<xml name="manutest_MetaboliteSpectralMatcher">
    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="mzml" value="spectra.mzML"/>

    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
  </output_collection>
</test>
</xml>
<xml name="manutest_OpenSwathDIAPreScoring">
  <!-- data from a test that included all the needed test files -->
  <test>
    <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"/>
    </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"/>
    </output_collection>
  </test>
</xml>
<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
<xml name="manutest_OpenSwathFileSplitter">
  <test expect_num_outputs="3">
    <conditional name="adv_opts_cond">
      <param name="adv_opts_selector" value="advanced"/>
      <param name="force" value="false"/>
      <param name="test" value="true"/>
    </conditional>
    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
    <output_collection name="outputDirectory" count="6">
      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
    </output_collection>
    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
    <output name="ctd_out" ftype="xml">
      <assert_contents>
        <is_valid_xml/>
      </assert_contents>
    </output>
  </test>
</xml>
<xml name="manutest_OpenSwathRewriteToFeatureXML">
  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
    <param name="adv_opts_cond|test" 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="adv_opts_cond|adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|skip_db_check" 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_cond|test" 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="adv_opts_cond|adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|skip_db_check" value="true"/>
    <param name="out_type" value="mzid"/>
    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" 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 -->
    <param name="adv_opts_selector" value="advanced"/>

    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
  </test>
</xml>
<xml name="manutest_RTEvaluation">
  <!-- just chosen an arbitrary input and autgenerated output-->
  <test expect_num_outputs="1">
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>
    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
  </test>
</xml>
<xml name="manutest_SemanticValidator">
  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
    <param name="adv_opts_selector" value="advanced"/>

    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
    </output>
  </test>
</xml>
<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>