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fix tests skipping
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@bernt-matthias
bernt-matthias committed May 30, 2024
1 parent e4c5a6b commit 1925d19
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240 changes: 0 additions & 240 deletions tools/openms/OpenSwathAnalyzer.xml
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Expand Up @@ -1311,246 +1311,6 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hard
<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
</assert_stdout>
</test>
<!-- TOPP_OpenSwathAnalyzer_test_3 -->
<test expect_num_outputs="2">
<section name="adv_opts">
<param name="force" value="false"/>
<param name="test" value="true"/>
</section>
<param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
<param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
<output name="out" value="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
<param name="no_strict" value="false"/>
<conditional name="swath_files_cond">
<param name="swath_files" value="OpenSwathAnalyzer_3_swathfile.mzML.cached.tmp"/>
</conditional>
<param name="min_upper_edge_dist" value="0.0"/>
<section name="model">
<param name="type" value="linear"/>
<param name="symmetric_regression" value="false"/>
</section>
<section name="algorithm">
<param name="stop_report_after_feature" value="-1"/>
<param name="rt_extraction_window" value="-1.0"/>
<param name="rt_normalization_factor" value="1.0"/>
<param name="quantification_cutoff" value="0.0"/>
<param name="write_convex_hull" value="false"/>
<param name="spectrum_addition_method" value="simple"/>
<param name="add_up_spectra" value="1"/>
<param name="spacing_for_spectra_resampling" value="0.005"/>
<param name="uis_threshold_sn" value="-1"/>
<param name="uis_threshold_peak_area" value="0"/>
<param name="scoring_model" value="default"/>
<param name="im_extra_drift" value="0.0"/>
<param name="strict" value="true"/>
<section name="TransitionGroupPicker">
<param name="stop_after_feature" value="-1"/>
<param name="stop_after_intensity_ratio" value="0.0001"/>
<param name="min_peak_width" value="0.001"/>
<param name="peak_integration" value="original"/>
<param name="background_subtraction" value="none"/>
<param name="recalculate_peaks" value="false"/>
<param name="use_precursors" value="false"/>
<param name="use_consensus" value="true"/>
<param name="recalculate_peaks_max_z" value="1.0"/>
<param name="minimal_quality" value="-10000.0"/>
<param name="resample_boundary" value="15.0"/>
<param name="compute_peak_quality" value="false"/>
<param name="compute_peak_shape_metrics" value="false"/>
<param name="compute_total_mi" value="false"/>
<param name="boundary_selection_method" value="largest"/>
<section name="PeakPickerMRM">
<param name="sgolay_frame_length" value="15"/>
<param name="sgolay_polynomial_order" value="3"/>
<param name="gauss_width" value="50.0"/>
<param name="use_gauss" value="true"/>
<param name="peak_width" value="40.0"/>
<param name="signal_to_noise" value="1.0"/>
<param name="sn_win_len" value="1000.0"/>
<param name="sn_bin_count" value="30"/>
<param name="write_sn_log_messages" value="false"/>
<param name="remove_overlapping_peaks" value="false"/>
<param name="method" value="legacy"/>
</section>
<section name="PeakIntegrator">
<param name="integration_type" value="intensity_sum"/>
<param name="baseline_type" value="base_to_base"/>
<param name="fit_EMG" value="false"/>
</section>
</section>
<section name="DIAScoring">
<param name="dia_extraction_window" value="0.05"/>
<param name="dia_extraction_unit" value="Th"/>
<param name="dia_centroided" value="false"/>
<param name="dia_byseries_intensity_min" value="300.0"/>
<param name="dia_byseries_ppm_diff" value="10.0"/>
<param name="dia_nr_isotopes" value="4"/>
<param name="dia_nr_charges" value="4"/>
<param name="peak_before_mono_max_ppm_diff" value="20.0"/>
</section>
<section name="EMGScoring">
<param name="interpolation_step" value="0.2"/>
<param name="tolerance_stdev_bounding_box" value="3.0"/>
<param name="max_iteration" value="500"/>
<param name="init_mom" value="false"/>
<section name="statistics">
<param name="mean" value="1.0"/>
<param name="variance" value="1.0"/>
</section>
</section>
<section name="Scores">
<param name="use_shape_score" value="true"/>
<param name="use_coelution_score" value="true"/>
<param name="use_rt_score" value="true"/>
<param name="use_library_score" value="true"/>
<param name="use_elution_model_score" value="true"/>
<param name="use_intensity_score" value="true"/>
<param name="use_nr_peaks_score" value="true"/>
<param name="use_total_xic_score" value="true"/>
<param name="use_total_mi_score" value="false"/>
<param name="use_sn_score" value="true"/>
<param name="use_mi_score" value="false"/>
<param name="use_dia_scores" value="true"/>
<param name="use_ms1_correlation" value="false"/>
<param name="use_sonar_scores" value="false"/>
<param name="use_ion_mobility_scores" value="false"/>
<param name="use_ms1_fullscan" value="false"/>
<param name="use_ms1_mi" value="false"/>
<param name="use_uis_scores" value="false"/>
<param name="use_ionseries_scores" value="true"/>
<param name="use_ms2_isotope_scores" value="true"/>
</section>
</section>
<param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
<output name="ctd_out" ftype="xml">
<assert_contents>
<is_valid_xml/>
</assert_contents>
</output>
<assert_stdout>
<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
</assert_stdout>
</test>
<!-- TOPP_OpenSwathAnalyzer_test_4 -->
<test expect_num_outputs="2">
<section name="adv_opts">
<param name="force" value="false"/>
<param name="test" value="true"/>
</section>
<param name="in" value="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp"/>
<param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
<output name="out" value="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
<param name="no_strict" value="false"/>
<conditional name="swath_files_cond">
<param name="swath_files" value="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp"/>
</conditional>
<param name="min_upper_edge_dist" value="0.0"/>
<section name="model">
<param name="type" value="linear"/>
<param name="symmetric_regression" value="false"/>
</section>
<section name="algorithm">
<param name="stop_report_after_feature" value="-1"/>
<param name="rt_extraction_window" value="-1.0"/>
<param name="rt_normalization_factor" value="1.0"/>
<param name="quantification_cutoff" value="0.0"/>
<param name="write_convex_hull" value="false"/>
<param name="spectrum_addition_method" value="simple"/>
<param name="add_up_spectra" value="1"/>
<param name="spacing_for_spectra_resampling" value="0.005"/>
<param name="uis_threshold_sn" value="-1"/>
<param name="uis_threshold_peak_area" value="0"/>
<param name="scoring_model" value="default"/>
<param name="im_extra_drift" value="0.0"/>
<param name="strict" value="true"/>
<section name="TransitionGroupPicker">
<param name="stop_after_feature" value="-1"/>
<param name="stop_after_intensity_ratio" value="0.0001"/>
<param name="min_peak_width" value="0.001"/>
<param name="peak_integration" value="original"/>
<param name="background_subtraction" value="none"/>
<param name="recalculate_peaks" value="false"/>
<param name="use_precursors" value="false"/>
<param name="use_consensus" value="true"/>
<param name="recalculate_peaks_max_z" value="1.0"/>
<param name="minimal_quality" value="-10000.0"/>
<param name="resample_boundary" value="15.0"/>
<param name="compute_peak_quality" value="false"/>
<param name="compute_peak_shape_metrics" value="false"/>
<param name="compute_total_mi" value="false"/>
<param name="boundary_selection_method" value="largest"/>
<section name="PeakPickerMRM">
<param name="sgolay_frame_length" value="15"/>
<param name="sgolay_polynomial_order" value="3"/>
<param name="gauss_width" value="50.0"/>
<param name="use_gauss" value="true"/>
<param name="peak_width" value="40.0"/>
<param name="signal_to_noise" value="1.0"/>
<param name="sn_win_len" value="1000.0"/>
<param name="sn_bin_count" value="30"/>
<param name="write_sn_log_messages" value="false"/>
<param name="remove_overlapping_peaks" value="false"/>
<param name="method" value="legacy"/>
</section>
<section name="PeakIntegrator">
<param name="integration_type" value="intensity_sum"/>
<param name="baseline_type" value="base_to_base"/>
<param name="fit_EMG" value="false"/>
</section>
</section>
<section name="DIAScoring">
<param name="dia_extraction_window" value="0.05"/>
<param name="dia_extraction_unit" value="Th"/>
<param name="dia_centroided" value="false"/>
<param name="dia_byseries_intensity_min" value="300.0"/>
<param name="dia_byseries_ppm_diff" value="10.0"/>
<param name="dia_nr_isotopes" value="4"/>
<param name="dia_nr_charges" value="4"/>
<param name="peak_before_mono_max_ppm_diff" value="20.0"/>
</section>
<section name="EMGScoring">
<param name="interpolation_step" value="0.2"/>
<param name="tolerance_stdev_bounding_box" value="3.0"/>
<param name="max_iteration" value="500"/>
<param name="init_mom" value="false"/>
<section name="statistics">
<param name="mean" value="1.0"/>
<param name="variance" value="1.0"/>
</section>
</section>
<section name="Scores">
<param name="use_shape_score" value="true"/>
<param name="use_coelution_score" value="true"/>
<param name="use_rt_score" value="true"/>
<param name="use_library_score" value="true"/>
<param name="use_elution_model_score" value="true"/>
<param name="use_intensity_score" value="true"/>
<param name="use_nr_peaks_score" value="true"/>
<param name="use_total_xic_score" value="true"/>
<param name="use_total_mi_score" value="false"/>
<param name="use_sn_score" value="true"/>
<param name="use_mi_score" value="false"/>
<param name="use_dia_scores" value="true"/>
<param name="use_ms1_correlation" value="false"/>
<param name="use_sonar_scores" value="false"/>
<param name="use_ion_mobility_scores" value="false"/>
<param name="use_ms1_fullscan" value="false"/>
<param name="use_ms1_mi" value="false"/>
<param name="use_uis_scores" value="false"/>
<param name="use_ionseries_scores" value="true"/>
<param name="use_ms2_isotope_scores" value="true"/>
</section>
</section>
<param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
<output name="ctd_out" ftype="xml">
<assert_contents>
<is_valid_xml/>
</assert_contents>
</output>
<assert_stdout>
<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
</assert_stdout>
</test>
</tests>
<help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
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2 changes: 1 addition & 1 deletion tools/openms/get_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
r"OpenSwathMzMLFileCacher .*-convert_back", # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
r"MaRaClusterAdapter.*-consensus_out", # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ", # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
r'TOPP_OpenSwathAnalyzer_test_3 |TOPP_OpenSwathAnalyzer_test_4 ', # no suppert for cached mzML
r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$', # no suppert for cached mzML
r'TOPP_SiriusAdapter_[0-9]+$', # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway
r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$' # Skip AssayGeneratorMetabo tests using Sirius https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools)
]
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