comparison macros_test.xml @ 17:abffdfee3021 draft

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

16:01dbaf6a57e0

    <param name="test" value="true"/>
  </conditional>
  <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"/>
  </output_collection>
  <output name="ctd_out" ftype="xml">
    <assert_contents>
      <is_valid_xml/>
    </assert_contents>

  <!-- 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">

    <param name="in" ftype="mzml" value="spectra.mzML"/>
    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
    <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
  </test>
</xml>
<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"/>
    <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"/>
    <param name="adv_opts_cond|test" value="true"/>

17:abffdfee3021

    <param name="test" value="true"/>
  </conditional>
  <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_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>
      <is_valid_xml/>
    </assert_contents>

  <!-- 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" 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_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
      <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
    </output_collection>
  </test>
</xml>
<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
<xml name="manutest_OpenSwathFileSplitter">

    <param name="in" ftype="mzml" value="spectra.mzML"/>
    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
    <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"/>
    <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>
  <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 -->
    <param name="adv_opts_selector" value="advanced"/>
    <param name="adv_opts_cond|test" value="true"/>