comparison macros_autotest.xml @ 13:71a6c870aa48 draft

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

12:24fd374cbffc

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

</xml>
  <xml name="autotest_CometAdapter">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="fragment_bin_tolerance" value="1.0005"/>
        <param name="fragment_bin_offset" value="0.25"/>
        <param name="instrument" value="high_res"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="1000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

        <param name="remove_precursor_peak" value="no"/>
        <param name="remove_precursor_tolerance" value="1.5"/>
        <param name="clear_mz_range" value="0:0"/>
        <param name="max_variable_mods_in_peptide" value="5"/>
        <param name="require_variable_mod" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="spectra_comet.mzML"/>
      <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="proteins.fasta"/>
      <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="3.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error" value="off"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="allowed_missed_cleavages" value="1"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep any known"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="fragment_bin_tolerance" value="1.0005"/>
        <param name="fragment_bin_offset" value="0.25"/>
        <param name="instrument" value="high_res"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="1000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

        <param name="remove_precursor_peak" value="no"/>
        <param name="remove_precursor_tolerance" value="1.5"/>
        <param name="clear_mz_range" value="0:0"/>
        <param name="max_variable_mods_in_peptide" value="5"/>
        <param name="require_variable_mod" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="CometAdapter_2_prepared.mzML"/>
      <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="CometAdapter_2_in.fasta"/>
      <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="3.0"/>
      <param name="precursor_error_units" value="Da"/>
      <param name="isotope_error" value="off"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="allowed_missed_cleavages" value="1"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep any known"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="fragment_bin_tolerance" value="0.02"/>
        <param name="fragment_bin_offset" value="0.0"/>
        <param name="instrument" value="high_res"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="20000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

      <param name="database" value="CometAdapter_3.fasta"/>
      <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="5.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error" value="off"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="allowed_missed_cleavages" value="3"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep known search unknown"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
      <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="PEPMatrix"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_2_input.featureXML"/>
      <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="average"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_3_input.consensusXML"/>
      <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="PEPMatrix"/>
      <section name="filter">
        <param name="considered_hits" value="6"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="PEPIons"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.5"/>
        <param name="count_empty" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      <param name="isotope_error" value=""/>
      <param name="run_percolator" value="false"/>
      <param name="enzyme" value="trypsin"/>
      <param name="digestion" value="full-digest"/>
      <param name="allowed_missed_cleavages" value="0"/>
      <param name="decoy_format" value="shuffle"/>
      <param name="keep_terminal_aminos" value="NC"/>
      <param name="cterm_modifications" value=""/>
      <param name="nterm_modifications" value=""/>
      <param name="modifications" value=""/>
      <param name="test_fdr" value="0.01"/>

      <param name="in" value="DatabaseFilter_3.fasta"/>
      <param name="id" value="DatabaseFilter_3.mzid"/>
      <param name="method" value="blacklist"/>
      <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      </output>
    </test>
  </xml>
  <xml name="autotest_DeMeanderize">
</xml>
  <xml name="autotest_Digestor">
</xml>
  <xml name="autotest_DTAExtractor">
    <test expect_num_outputs="1">
      <conditional name="adv_opts_cond">

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_1_input.idXML"/>
      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="protein_fdr" value="false"/>
      <param name="greedy_group_resolution" value="none"/>
      <param name="max_psms_extreme_probability" value="1.0"/>
      <section name="algorithm">
        <param name="psm_probability_cutoff" value="0.001"/>
        <param name="top_PSMs" value="1"/>
        <param name="update_PSM_probabilities" value="true"/>
        <param name="user_defined_priors" value="false"/>
        <param name="annotate_group_probabilities" value="true"/>
        <param name="use_ids_outside_features" value="false"/>
        <section name="model_parameters">

          <param name="p_norm_inference" value="1.0"/>
        </section>
        <section name="param_optimize">
          <param name="aucweight" value="0.3"/>
          <param name="conservative_fdr" value="true"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <section name="model">
        <param name="type" value="none"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

      <section name="model">
        <param name="type" value="symmetric"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="FeatureFinderIdentification_1_input.mzML"/>
      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
      <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="extract">
        <param name="batch_size" value="10"/>
        <param name="mz_window" value="0.1"/>
        <param name="n_isotopes" value="2"/>
        <param name="isotope_pmin" value="0.0"/>
        <param name="rt_quantile" value="0.95"/>
        <param name="rt_window" value="0.0"/>
      </section>
      <section name="detect">
        <param name="peak_width" value="60.0"/>
        <param name="min_peak_width" value="0.2"/>
        <param name="signal_to_noise" value="0.8"/>
        <param name="mapping_tolerance" value="0.0"/>
      </section>
      <section name="svm">
        <param name="samples" value="0"/>
        <param name="no_selection" value="false"/>
        <param name="kernel" value="RBF"/>
        <param name="xval" value="5"/>
        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
        <param name="epsilon" value="0.001"/>
        <param name="cache_size" value="100.0"/>
        <param name="no_shrinking" value="false"/>
        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
        <param name="min_prob" value="0.0"/>
      </section>
      <section name="model">
        <param name="type" value="none"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

      <section name="model">
        <param name="type" value="symmetric"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

        <param name="log2_states_precalc" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_1_input.idXML"/>
      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="separate_runs" value="false"/>
      <param name="greedy_group_resolution" value="false"/>
      <param name="no_cleanup" value="false"/>
      <param name="all_PSMs" value="false"/>
      <param name="group_level" value="false"/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileConverter_30_output.mzML"/>
      <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="PepXMLFile_test.pepxml"/>
      <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_3_input.protXML"/>
      <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_6_input1.pepXML"/>
      <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_7_input1.xml"/>
      <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_8_input.mzid"/>
      <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_9_input.idXML"/>
      <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_10_input.pepXML"/>
      <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
      <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_16_input.pepXML"/>
      <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_17_input.idXML"/>
      <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_18_input.idXML"/>
      <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_19_input.idXML"/>
      <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_20_input.idXML"/>
      <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_21_input.idXML"/>
      <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.01"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_23_input.mzid"/>
      <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_24_input.pep.xml"/>
      <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_25_input.idXML"/>
      <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_26_input.mzid"/>
      <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="out_type" value="idXML"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="proteins" value="IDFilter_1_input.fas"/>
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="32.0"/>
        <param name="prot" value="25.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="32.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="25.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="25.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.05"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.3"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_output.idXML"/>
      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="new_score" value="Percolator_PEP"/>
      <param name="new_score_orientation" value="lower_better"/>
      <param name="new_score_type" value="Posterior Error Probability"/>
      <param name="old_score" value="Percolator_qvalue"/>
      <param name="proteins" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="new_score" value="Posterior Probability_score"/>
      <param name="new_score_orientation" value="higher_better"/>
      <param name="new_score_type" value="Posterior Probability"/>
      <param name="old_score" value=""/>
      <param name="proteins" value="true"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

      </output>
    </test>
  </xml>
  <xml name="autotest_LabeledEval">
</xml>
  <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
    <test expect_num_outputs="2">
      <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="PeakPickerHiRes_RandomAccess_input.mzML"/>
      <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <param name="signal_to_noise" value="1.0"/>
        <param name="spacing_difference_gap" value="4.0"/>
        <param name="spacing_difference" value="1.5"/>
        <param name="missing" value="1"/>
        <param name="ms_levels" value="1"/>
        <param name="report_FWHM" value="false"/>
        <param name="report_FWHM_unit" value="relative"/>
        <section name="SignalToNoise">
          <param name="max_intensity" value="-1"/>
          <param name="auto_max_stdev_factor" value="3.0"/>
          <param name="auto_max_percentile" value="95"/>
          <param name="auto_mode" value="0"/>
          <param name="win_len" value="200.0"/>
          <param name="bin_count" value="30"/>
          <param name="min_required_elements" value="10"/>
          <param name="noise_for_empty_window" value="1e+20"/>
          <param name="write_log_messages" 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>
    </test>
  </xml>
  <xml name="autotest_LowMemPeakPickerHiRes">
    <test expect_num_outputs="2">
      <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="PeakPickerHiRes_input.mzML"/>
      <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <param name="signal_to_noise" value="1.0"/>
        <param name="spacing_difference_gap" value="4.0"/>
        <param name="spacing_difference" value="1.5"/>
        <param name="missing" value="1"/>
        <param name="ms_levels" value="1"/>
        <param name="report_FWHM" value="false"/>
        <param name="report_FWHM_unit" value="relative"/>
        <section name="SignalToNoise">
          <param name="max_intensity" value="-1"/>
          <param name="auto_max_stdev_factor" value="3.0"/>
          <param name="auto_max_percentile" value="95"/>
          <param name="auto_mode" value="0"/>
          <param name="win_len" value="200.0"/>
          <param name="bin_count" value="30"/>
          <param name="min_required_elements" value="10"/>
          <param name="noise_for_empty_window" value="1e+20"/>
          <param name="write_log_messages" 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>
    </test>
  </xml>
  <xml name="autotest_LuciphorAdapter">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>

          <param name="interpolation_type" value="cspline"/>
          <param name="extrapolation_type" value="two-point-linear"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_MapNormalizer">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MascotAdapter_1_input.mzData"/>
      <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="mascot_in" value="true"/>
      <param name="mascot_out" value="false"/>
      <param name="instrument" value="ESI-TRAP"/>
      <param name="precursor_mass_tolerance" value="1.3"/>
      <param name="peak_mass_tolerance" value="0.3"/>
      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="mascot_in" value="false"/>
      <param name="mascot_out" value="true"/>
      <param name="instrument" value="Default"/>
      <param name="precursor_mass_tolerance" value="2.0"/>
      <param name="peak_mass_tolerance" value="1.0"/>
      <param name="taxonomy" value="All entries"/>
      <param name="modifications" value=""/>

      <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="MassCalculator_1_input.txt" ftype="txt"/>
      <param name="in_seq" value=""/>
      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/>
      <param name="charge" value="0 1"/>
      <param name="format" value="table"/>
      <param name="average_mass" value="false"/>
      <param name="fragment_type" value="full"/>
      <param name="separator" value=","/>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
      <param name="charge" value="1 2 3"/>
      <param name="format" value="list"/>
      <param name="average_mass" value="false"/>
      <param name="fragment_type" value="full"/>
      <param name="separator" value=""/>

        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_MetaboliteAdductDecharger">
</xml>
  <xml name="autotest_MetaboliteSpectralMatcher">
</xml>
  <xml name="autotest_MetaProSIP">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">

  <xml name="autotest_MSFraggerAdapter"/>
  <xml name="autotest_MSGFPlusAdapter">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="legacy_conversion" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="spectra.mzML"/>
      <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
      <param name="database" value="proteins.fasta"/>
      <param name="add_decoys" value="false"/>
      <param name="precursor_mass_tolerance" value="10.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error_range" value="0,1"/>
      <param name="fragment_method" value="from_spectrum"/>
      <param name="instrument" value="high_res"/>

      <param name="min_peptide_length" value="6"/>
      <param name="max_peptide_length" value="40"/>
      <param name="matches_per_spec" value="1"/>
      <param name="add_features" value="false"/>
      <param name="max_mods" value="2"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value="Oxidation (M)"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MzTabExporter_3_input.featureXML"/>
      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_OpenSwathFeatureXMLToTSV">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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"/>
        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

    <test expect_num_outputs="4">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="false"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="false"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
      <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <param name="use_rt_score" value="true"/>
          <param name="use_library_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
      <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <param name="use_rt_score" value="true"/>
          <param name="use_library_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cache"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cacheWorkingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="true"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="false"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="550.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
      <param name="tr_type" value=""/>
      <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
      <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="true"/>
      <param name="rt_extraction_window" value="-1.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.2"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="none"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
      <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="sqMass"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
      <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="2"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="true"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="false"/>

          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="2"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="false"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cache"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="false"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="4">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
      <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="use_ms1_traces" value="true"/>
        <param name="enable_uis_scoring" value="false"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="Th"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="true"/>
        <param name="irt_mz_extraction_window" value="0.05"/>
        <param name="irt_mz_extraction_window_unit" value="Th"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="250"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="0.05"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="0"/>
        <param name="uis_threshold_peak_area" value="0"/>
        <param name="scoring_model" value="default"/>
        <param name="im_extra_drift" value="0.0"/>
        <section name="TransitionGroupPicker">
          <param name="stop_after_feature" value="-1"/>
          <param name="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="true"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

        <param name="processOption" value="inmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="PeakPickerHiRes_input.mzML"/>
      <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <param name="signal_to_noise" value="1.0"/>
        <param name="spacing_difference_gap" value="4.0"/>
        <param name="spacing_difference" value="1.5"/>
        <param name="missing" value="1"/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="true"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="0"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="3"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="full"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="semi"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="false"/>
      <param name="aaa_max" value="3"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="true"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="full"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="true"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="false"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="full"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="allow_unmatched" value="false"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="Trypsin"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.5"/>
        <param name="trainFDR" value="0.5"/>
        <param name="maxiter" value="10"/>
        <param name="quick_validation" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="quick_validation" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="quick_validation" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="quick_validation" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.5"/>
        <param name="trainFDR" value="0.5"/>
        <param name="maxiter" value="10"/>
        <param name="quick_validation" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="merge_runs" value="all"/>
      <param name="annotate_indist_groups" value="true"/>
      <section name="Merging">
        <param name="annotate_origin" value="false"/>
      </section>
      <section name="Algorithm">
        <param name="min_peptides_per_protein" value="1"/>
        <param name="score_aggregation_method" value="maximum"/>
        <param name="treat_charge_variants_separately" value="true"/>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="ProteinQuantifier_input.consensusXML"/>
      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="top" value="3"/>
      <param name="average" value="sum"/>
      <param name="include_all" value="true"/>
      <param name="best_charge_and_fraction" value="false"/>
      <param name="greedy_group_resolution" value="false"/>

      <section name="format">
        <param name="separator" value=""/>
        <param name="quoting" value="double"/>
        <param name="replacement" value="_"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      <section name="FragmentMassError">
        <param name="unit" value="auto"/>
        <param name="tolerance" value="20.0"/>
      </section>
      <section name="MS2_id_rate">
        <param name="force_no_fdr" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      <param name="in" value="SimpleSearchEngine_1.mzML"/>
      <param name="database" value="SimpleSearchEngine_1.fasta"/>
      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <section name="Search">
        <param name="enzyme" value="Trypsin"/>
        <section name="precursor">
          <param name="mass_tolerance" value="5.0"/>
          <param name="mass_tolerance_unit" value="ppm"/>
          <param name="min_charge" value="2"/>
          <param name="max_charge" value="5"/>

        </section>
        <section name="modifications">
          <param name="fixed" value=""/>
          <param name="variable" value="Oxidation (M)"/>
          <param name="variable_max_per_peptide" value="2"/>
        </section>
        <section name="peptide">
          <param name="min_size" value="7"/>
          <param name="max_size" value="40"/>
          <param name="missed_cleavages" value="1"/>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="no_masstrace_info_isotope_pattern" value="false"/>
      </section>
      <section name="sirius">
        <param name="profile" value="qtof"/>
        <param name="candidates" value="5"/>
        <param name="database" value="all"/>
        <param name="noise" value="0"/>
        <param name="ppm_max" value="10"/>
        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="cores" value="1"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

    </test>
  </xml>
  <xml name="autotest_SpectraMerger">
</xml>
  <xml name="autotest_SpectraSTSearchAdapter"/>
  <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
</xml>
  <xml name="autotest_TargetedFileConverter">
    <test expect_num_outputs="2">
      <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="TextExporter_1_input.featureXML"/>
      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_2_input.consensusXML"/>
      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

        <param name="sort_by_size" value="true"/>
      </section>
      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_3_input.idXML"/>
      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_3_input.idXML"/>
      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_5_input.idXML"/>
      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_6_input.featureXML"/>
      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_7_input.consensusXML"/>
      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="RT_then_MZ"/>
        <param name="sort_by_maps" value="true"/>
        <param name="sort_by_size" value="true"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_1_input.featureXML"/>
      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_9_input.idXML"/>
      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TOFCalibration_1_input.mzML"/>
      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
      <param name="peak_data" value="false"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>

        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TOFCalibration_2_input.mzML"/>
      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
      <param name="peak_data" value="true"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
<xml name="autotest_InspectAdapter"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_RTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_DigestorMotif"/><xml name="autotest_PTPredict"/></macros>

13:71a6c870aa48

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="100"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

</xml>
  <xml name="autotest_CometAdapter">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="second_enzyme" value=""/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="1000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

        <param name="remove_precursor_peak" value="no"/>
        <param name="remove_precursor_tolerance" value="1.5"/>
        <param name="clear_mz_range" value="0:0"/>
        <param name="max_variable_mods_in_peptide" value="5"/>
        <param name="require_variable_mod" value="false"/>
        <param name="force" value="true"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="spectra_comet.mzML"/>
      <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="proteins.fasta"/>
      <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="3.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error" value="off"/>
      <param name="fragment_mass_tolerance" value="0.50025"/>
      <param name="fragment_error_units" value="Da"/>
      <param name="fragment_bin_offset" value="0.25"/>
      <param name="instrument" value="high_res"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="missed_cleavages" value="1"/>
      <param name="min_peptide_length" value="5"/>
      <param name="max_peptide_length" value="63"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep any known"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value=""/>
      <param name="binary_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="second_enzyme" value=""/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="1000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

        <param name="remove_precursor_peak" value="no"/>
        <param name="remove_precursor_tolerance" value="1.5"/>
        <param name="clear_mz_range" value="0:0"/>
        <param name="max_variable_mods_in_peptide" value="5"/>
        <param name="require_variable_mod" value="false"/>
        <param name="force" value="true"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="CometAdapter_2_prepared.mzML"/>
      <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="CometAdapter_2_in.fasta"/>
      <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="3.0"/>
      <param name="precursor_error_units" value="Da"/>
      <param name="isotope_error" value="off"/>
      <param name="fragment_mass_tolerance" value="0.50025"/>
      <param name="fragment_error_units" value="Da"/>
      <param name="fragment_bin_offset" value="0.25"/>
      <param name="instrument" value="high_res"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="missed_cleavages" value="1"/>
      <param name="min_peptide_length" value="5"/>
      <param name="max_peptide_length" value="63"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep any known"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value=""/>
      <param name="binary_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="second_enzyme" value=""/>
        <param name="digest_mass_range" value="600:5000"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="20000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>

      <param name="database" value="CometAdapter_3.fasta"/>
      <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="precursor_mass_tolerance" value="5.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error" value="off"/>
      <param name="fragment_mass_tolerance" value="0.01"/>
      <param name="fragment_error_units" value="Da"/>
      <param name="fragment_bin_offset" value="0.0"/>
      <param name="instrument" value="high_res"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="missed_cleavages" value="3"/>
      <param name="min_peptide_length" value="5"/>
      <param name="max_peptide_length" value="63"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep known search unknown"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
      <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
      <param name="binary_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="use_A_ions" value="false"/>
        <param name="use_B_ions" value="true"/>
        <param name="use_C_ions" value="false"/>
        <param name="use_X_ions" value="false"/>
        <param name="use_Y_ions" value="true"/>
        <param name="use_Z_ions" value="false"/>
        <param name="use_NL_ions" value="false"/>
        <param name="second_enzyme" value=""/>
        <param name="digest_mass_range" value="600:1200"/>
        <param name="max_precursor_charge" value="5"/>
        <param name="spectrum_batch_size" value="20000"/>
        <param name="mass_offsets" value="0.0"/>
        <param name="minimum_peaks" value="10"/>
        <param name="minimum_intensity" value="0.0"/>
        <param name="remove_precursor_peak" value="no"/>
        <param name="remove_precursor_tolerance" value="1.5"/>
        <param name="clear_mz_range" value="0:0"/>
        <param name="max_variable_mods_in_peptide" value="3"/>
        <param name="require_variable_mod" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
      <param name="precursor_mass_tolerance" value="5.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error" value="off"/>
      <param name="fragment_mass_tolerance" value="0.01"/>
      <param name="fragment_error_units" value="Da"/>
      <param name="fragment_bin_offset" value="0.0"/>
      <param name="instrument" value="high_res"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="num_enzyme_termini" value="fully"/>
      <param name="missed_cleavages" value="3"/>
      <param name="min_peptide_length" value="5"/>
      <param name="max_peptide_length" value="63"/>
      <param name="num_hits" value="5"/>
      <param name="precursor_charge" value="0:0"/>
      <param name="override_charge" value="keep known search unknown"/>
      <param name="ms_level" value="2"/>
      <param name="activation_method" value="ALL"/>
      <param name="max_fragment_charge" value="3"/>
      <param name="clip_nterm_methionine" value="false"/>
      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
      <param name="binary_modifications" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="PEPMatrix"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_2_input.featureXML"/>
      <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="average"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_3_input.consensusXML"/>
      <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="PEPMatrix"/>
      <section name="filter">
        <param name="considered_hits" value="6"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="PEPIons"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      </conditional>
      <param name="in" value="ConsensusID_1_input.idXML"/>
      <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="false"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.5"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="false"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="identity"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="ConsensusID_6_input.idXML"/>
      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="true"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="true"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>
      <section name="PEPMatrix">
        <param name="matrix" value="identity"/>
        <param name="penalty" value="5"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="ConsensusID_8_input.idXML"/>
      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="rt_delta" value="0.1"/>
      <param name="mz_delta" value="0.1"/>
      <param name="per_spectrum" value="true"/>
      <param name="algorithm" value="best"/>
      <section name="filter">
        <param name="considered_hits" value="0"/>
        <param name="min_support" value="0.0"/>
        <param name="count_empty" value="false"/>
        <param name="keep_old_scores" value="true"/>
      </section>
      <section name="PEPIons">
        <param name="mass_tolerance" value="0.5"/>
        <param name="min_shared" value="2"/>
      </section>

      <param name="isotope_error" value=""/>
      <param name="run_percolator" value="false"/>
      <param name="enzyme" value="trypsin"/>
      <param name="digestion" value="full-digest"/>
      <param name="allowed_missed_cleavages" value="0"/>
      <param name="decoy_format" value="peptide-reverse"/>
      <param name="keep_terminal_aminos" value="NC"/>
      <param name="cterm_modifications" value=""/>
      <param name="nterm_modifications" value=""/>
      <param name="modifications" value=""/>
      <param name="test_fdr" value="0.01"/>

      <param name="in" value="DatabaseFilter_3.fasta"/>
      <param name="id" value="DatabaseFilter_3.mzid"/>
      <param name="method" value="blacklist"/>
      <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_DatabaseSuitability">
    <test expect_num_outputs="2">
      <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_id" value="DatabaseSuitability_in_id.idXML"/>
      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <section name="algorithm">
        <param name="no_rerank" value="false"/>
        <param name="reranking_cutoff_percentile" value="0.01"/>
        <param name="FDR" value="0.8"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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_id" value="DatabaseSuitability_in_id.idXML"/>
      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <section name="algorithm">
        <param name="no_rerank" value="false"/>
        <param name="reranking_cutoff_percentile" value="0.9"/>
        <param name="FDR" value="1.0"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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_id" value="DatabaseSuitability_in_id.idXML"/>
      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <section name="algorithm">
        <param name="no_rerank" value="true"/>
        <param name="reranking_cutoff_percentile" value="0.01"/>
        <param name="FDR" value="0.9"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      </output>
    </test>
  </xml>
  <xml name="autotest_DeMeanderize">
</xml>
  <xml name="autotest_DigestorMotif">
</xml>
  <xml name="autotest_Digestor">
</xml>
  <xml name="autotest_DTAExtractor">
    <test expect_num_outputs="1">
      <conditional name="adv_opts_cond">

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_1_input.idXML"/>
      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="out_type" value="idxml"/>
      <param name="protein_fdr" value="false"/>
      <param name="greedy_group_resolution" value="none"/>
      <param name="max_psms_extreme_probability" value="1.0"/>
      <section name="algorithm">
        <param name="psm_probability_cutoff" value="0.001"/>
        <param name="top_PSMs" value="1"/>
        <param name="keep_best_PSM_only" value="true"/>
        <param name="update_PSM_probabilities" value="true"/>
        <param name="user_defined_priors" value="false"/>
        <param name="annotate_group_probabilities" value="true"/>
        <param name="use_ids_outside_features" value="false"/>
        <section name="model_parameters">

          <param name="p_norm_inference" value="1.0"/>
        </section>
        <section name="param_optimize">
          <param name="aucweight" value="0.3"/>
          <param name="conservative_fdr" value="true"/>
          <param name="regularized_fdr" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="conservative_fdr" value="true"/>
        <param name="min_psms_extreme_probability" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="Epifany_2_input.consensusXML"/>
      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="protein_fdr" value="false"/>
      <param name="greedy_group_resolution" value="none"/>
      <param name="max_psms_extreme_probability" value="1.0"/>
      <section name="algorithm">
        <param name="psm_probability_cutoff" value="0.001"/>
        <param name="top_PSMs" value="1"/>
        <param name="keep_best_PSM_only" value="true"/>
        <param name="update_PSM_probabilities" value="true"/>
        <param name="user_defined_priors" value="false"/>
        <param name="annotate_group_probabilities" value="true"/>
        <param name="use_ids_outside_features" value="false"/>
        <section name="model_parameters">
          <param name="prot_prior" value="0.7"/>
          <param name="pep_emission" value="0.1"/>
          <param name="pep_spurious_emission" value="0.001"/>
          <param name="pep_prior" value="0.1"/>
          <param name="regularize" value="false"/>
          <param name="extended_model" value="false"/>
        </section>
        <section name="loopy_belief_propagation">
          <param name="scheduling_type" value="priority"/>
          <param name="convergence_threshold" value="1e-05"/>
          <param name="dampening_lambda" value="0.001"/>
          <param name="max_nr_iterations" value="2147483647"/>
          <param name="p_norm_inference" value="1.0"/>
        </section>
        <section name="param_optimize">
          <param name="aucweight" value="0.3"/>
          <param name="conservative_fdr" value="true"/>
          <param name="regularized_fdr" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="conservative_fdr" value="true"/>
        <param name="min_psms_extreme_probability" value="0.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="Epifany_2_input.consensusXML"/>
      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="protein_fdr" value="false"/>
      <param name="greedy_group_resolution" value="none"/>
      <param name="max_psms_extreme_probability" value="1.0"/>
      <section name="algorithm">
        <param name="psm_probability_cutoff" value="0.001"/>
        <param name="top_PSMs" value="1"/>
        <param name="keep_best_PSM_only" value="false"/>
        <param name="update_PSM_probabilities" value="true"/>
        <param name="user_defined_priors" value="false"/>
        <param name="annotate_group_probabilities" value="true"/>
        <param name="use_ids_outside_features" value="false"/>
        <section name="model_parameters">
          <param name="prot_prior" value="0.7"/>
          <param name="pep_emission" value="0.1"/>
          <param name="pep_spurious_emission" value="0.001"/>
          <param name="pep_prior" value="0.1"/>
          <param name="regularize" value="false"/>
          <param name="extended_model" value="false"/>
        </section>
        <section name="loopy_belief_propagation">
          <param name="scheduling_type" value="priority"/>
          <param name="convergence_threshold" value="1e-05"/>
          <param name="dampening_lambda" value="0.001"/>
          <param name="max_nr_iterations" value="2147483647"/>
          <param name="p_norm_inference" value="1.0"/>
        </section>
        <section name="param_optimize">
          <param name="aucweight" value="0.3"/>
          <param name="conservative_fdr" value="true"/>
          <param name="regularized_fdr" value="true"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <section name="model">
        <param name="type" value="none"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <param name="each_trace" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

      <section name="model">
        <param name="type" value="symmetric"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <param name="each_trace" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

      <section name="model">
        <param name="type" value="symmetric"/>
        <param name="add_zeros" value="0.2"/>
        <param name="unweighted_fit" value="false"/>
        <param name="no_imputation" value="false"/>
        <param name="each_trace" value="false"/>
        <section name="check">
          <param name="min_area" value="1.0"/>
          <param name="boundaries" value="0.5"/>
          <param name="width" value="10.0"/>
          <param name="asymmetry" value="10.0"/>

        <param name="log2_states_precalc" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_1_input.idXML"/>
      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="separate_runs" value="false"/>
      <param name="greedy_group_resolution" value="false"/>
      <param name="no_cleanup" value="false"/>
      <param name="all_PSMs" value="false"/>
      <param name="group_level" value="false"/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileConverter_30_output.mzML"/>
      <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="UID_postprocessing" value="ensure"/>
        <param name="TIC_DTA2D" value="false"/>
        <param name="MGF_compact" value="false"/>
        <param name="force_MaxQuant_compatibility" value="false"/>
        <param name="convert_to_chromatograms" value="false"/>
        <param name="force_TPP_compatibility" value="false"/>
        <param name="change_im_format" value="none"/>
        <param name="write_scan_index" value="true"/>
        <param name="lossy_compression" value="false"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="false"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileConverter_32_input.mzML"/>
      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="PepXMLFile_test.pepxml"/>
      <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_3_input.protXML"/>
      <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
      <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_6_input1.pepXML"/>
      <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_7_input1.xml"/>
      <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_8_input.mzid"/>
      <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_9_input.idXML"/>
      <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_10_input.pepXML"/>
      <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
      <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_input.psms"/>
      <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_16_input.pepXML"/>
      <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_17_input.idXML"/>
      <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_18_input.idXML"/>
      <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_19_input.idXML"/>
      <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_20_input.idXML"/>
      <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_21_input.idXML"/>
      <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.01"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
      <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_23_input.mzid"/>
      <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_24_input.pep.xml"/>
      <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_25_input.idXML"/>
      <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>

        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_26_input.mzid"/>
      <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="out_type" value="idXML"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="out_type" value="FASTA"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="-1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="out_type" value="FASTA"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="true"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="out_type" value="FASTA"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="true"/>
        <param name="number_of_hits" value="2"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_27_input.idXML"/>
      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="out_type" value="FASTA"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="ignore_proteins_per_peptide" value="false"/>
        <param name="scan_regex" value=""/>
        <param name="no_spectra_data_override" value="false"/>
        <param name="no_spectra_references_override" value="false"/>
        <param name="add_ionmatch_annotation" value="0.0"/>
        <param name="concatenate_peptides" value="false"/>
        <param name="number_of_hits" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_31_input.mzid"/>
      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="out_type" value="idXML"/>
      <param name="mz_name" value=""/>
      <param name="peptideprophet_analyzed" value="false"/>
      <param name="score_type" value="qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="proteins" value="IDFilter_1_input.fas"/>
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="32.0"/>
        <param name="prot" value="25.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="32.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="25.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="25.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.05"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.3"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>
      </section>
      <section name="blacklist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>
      </section>
      <section name="in_silico_digestion">
        <param name="enzyme" value="Trypsin"/>
        <param name="specificity" value="full"/>
        <param name="missed_cleavages" value="-1"/>
        <param name="methionine_cleavage" value="false"/>
      </section>
      <section name="missed_cleavages">
        <param name="number_of_missed_cleavages" value=":"/>
        <param name="enzyme" value="Trypsin"/>
      </section>
      <section name="rt">
        <param name="p_value" value="0.0"/>
        <param name="p_value_1st_dim" value="0.0"/>
      </section>
      <section name="mz">
        <param name="error" value="-1.0"/>
        <param name="unit" value="ppm"/>
      </section>
      <section name="best">
        <param name="n_peptide_hits" value="0"/>
        <param name="n_protein_hits" value="0"/>
        <param name="strict" value="false"/>
        <param name="n_to_m_peptide_hits" value=":"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="remove_duplicate_psm" value="false"/>
        <param name="remove_peptide_hits_by_metavalue" value=""/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDMapper_2_output.consensusXML"/>
      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="var_mods" value="false"/>
      <param name="remove_shared_peptides" value="false"/>
      <param name="keep_unreferenced_protein_hits" value="false"/>
      <param name="remove_decoys" value="false"/>
      <param name="delete_unreferenced_peptide_hits" value="false"/>
      <section name="precursor">
        <param name="rt" value=":"/>
        <param name="mz" value=":"/>
        <param name="length" value=":"/>
        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.0"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>
      </section>
      <section name="blacklist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>
      </section>
      <section name="in_silico_digestion">
        <param name="enzyme" value="Trypsin"/>
        <param name="specificity" value="full"/>
        <param name="missed_cleavages" value="-1"/>
        <param name="methionine_cleavage" value="false"/>
      </section>
      <section name="missed_cleavages">
        <param name="number_of_missed_cleavages" value=":"/>
        <param name="enzyme" value="Trypsin"/>
      </section>
      <section name="rt">
        <param name="p_value" value="0.0"/>
        <param name="p_value_1st_dim" value="0.0"/>
      </section>
      <section name="mz">
        <param name="error" value="-1.0"/>
        <param name="unit" value="ppm"/>
      </section>
      <section name="best">
        <param name="n_peptide_hits" value="0"/>
        <param name="n_protein_hits" value="0"/>
        <param name="strict" value="false"/>
        <param name="n_to_m_peptide_hits" value=":"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="remove_duplicate_psm" value="false"/>
        <param name="remove_peptide_hits_by_metavalue" value=""/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="Epifany_3_out.consensusXML"/>
      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="var_mods" value="false"/>
      <param name="remove_shared_peptides" value="false"/>
      <param name="keep_unreferenced_protein_hits" value="false"/>
      <param name="remove_decoys" value="false"/>
      <param name="delete_unreferenced_peptide_hits" value="false"/>
      <section name="precursor">
        <param name="rt" value=":"/>
        <param name="mz" value=":"/>
        <param name="length" value=":"/>
        <param name="charge" value=":"/>
      </section>
      <section name="score">
        <param name="pep" value="0.0"/>
        <param name="prot" value="0.0"/>
        <param name="protgroup" value="0.99"/>
      </section>
      <section name="whitelist">
        <param name="protein_accessions" value=""/>
        <param name="ignore_modifications" value="false"/>
        <param name="modifications" value=""/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDFileConverter_12_output.idXML"/>
      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="proteins" value="false"/>
      <param name="new_score" value="Percolator_PEP"/>
      <param name="new_score_orientation" value="lower_better"/>
      <param name="new_score_type" value="Posterior Error Probability"/>
      <param name="old_score" value="Percolator_qvalue"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="proteins" value="true"/>
      <param name="new_score" value="Posterior Probability_score"/>
      <param name="new_score_orientation" value="higher_better"/>
      <param name="new_score_type" value="Posterior Probability"/>
      <param name="old_score" value=""/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

      </output>
    </test>
  </xml>
  <xml name="autotest_LabeledEval">
</xml>
  <xml name="autotest_LuciphorAdapter">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>

          <param name="interpolation_type" value="cspline"/>
          <param name="extrapolation_type" value="two-point-linear"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="true"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
      <output_collection name="out" count="1"/>
      <output_collection name="trafo_out" count="1"/>
      <section name="reference">
        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
        <param name="index" value="0"/>
      </section>
      <section name="algorithm">
        <param name="score_cutoff" value="false"/>
        <param name="min_score" value="0.05"/>
        <param name="min_run_occur" value="2"/>
        <param name="max_rt_shift" value="0.5"/>
        <param name="use_unassigned_peptides" value="true"/>
        <param name="use_feature_rt" value="false"/>
      </section>
      <section name="model">
        <param name="type" value="b_spline"/>
        <section name="linear">
          <param name="symmetric_regression" value="false"/>
          <param name="x_weight" value=""/>
          <param name="y_weight" value=""/>
          <param name="x_datum_min" value="1e-15"/>
          <param name="x_datum_max" value="1000000000000000.0"/>
          <param name="y_datum_min" value="1e-15"/>
          <param name="y_datum_max" value="1000000000000000.0"/>
        </section>
        <section name="b_spline">
          <param name="wavelength" value="0.0"/>
          <param name="num_nodes" value="5"/>
          <param name="extrapolate" value="linear"/>
          <param name="boundary_condition" value="2"/>
        </section>
        <section name="lowess">
          <param name="span" value="0.666666666666667"/>
          <param name="num_iterations" value="3"/>
          <param name="delta" value="-1.0"/>
          <param name="interpolation_type" value="cspline"/>
          <param name="extrapolation_type" value="four-point-linear"/>
        </section>
        <section name="interpolated">
          <param name="interpolation_type" value="cspline"/>
          <param name="extrapolation_type" value="two-point-linear"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
      <output_collection name="out" count="3"/>
      <section name="algorithm">
        <param name="model_type" value="b_spline"/>
        <section name="model">
          <param name="type" value="b_spline"/>
          <section name="linear">
            <param name="symmetric_regression" value="false"/>
            <param name="x_weight" value=""/>
            <param name="y_weight" value=""/>
            <param name="x_datum_min" value="1e-15"/>
            <param name="x_datum_max" value="1000000000000000.0"/>
            <param name="y_datum_min" value="1e-15"/>
            <param name="y_datum_max" value="1000000000000000.0"/>
          </section>
          <section name="b_spline">
            <param name="wavelength" value="0.0"/>
            <param name="num_nodes" value="5"/>
            <param name="extrapolate" value="linear"/>
            <param name="boundary_condition" value="2"/>
          </section>
          <section name="lowess">
            <param name="span" value="0.666666666666667"/>
            <param name="num_iterations" value="3"/>
            <param name="delta" value="-1.0"/>
            <param name="interpolation_type" value="cspline"/>
            <param name="extrapolation_type" value="four-point-linear"/>
          </section>
          <section name="interpolated">
            <param name="interpolation_type" value="cspline"/>
            <param name="extrapolation_type" value="two-point-linear"/>
          </section>
        </section>
        <section name="align_algorithm">
          <param name="score_cutoff" value="false"/>
          <param name="min_score" value="0.05"/>
          <param name="min_run_occur" value="2"/>
          <param name="max_rt_shift" value="0.5"/>
          <param name="use_unassigned_peptides" value="true"/>
          <param name="use_feature_rt" value="true"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_MapNormalizer">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MascotAdapter_1_input.mzData"/>
      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
      <param name="out_type" value="mgf"/>
      <param name="instrument" value="ESI-TRAP"/>
      <param name="precursor_mass_tolerance" value="1.3"/>
      <param name="peak_mass_tolerance" value="0.3"/>
      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="out_type" value="idXML"/>
      <param name="instrument" value="Default"/>
      <param name="precursor_mass_tolerance" value="2.0"/>
      <param name="peak_mass_tolerance" value="1.0"/>
      <param name="taxonomy" value="All entries"/>
      <param name="modifications" value=""/>

      <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="MassCalculator_1_input.tsv" ftype="tabular"/>
      <param name="in_seq" value=""/>
      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="charge" value="0 1"/>
      <param name="format" value="table"/>
      <param name="average_mass" value="false"/>
      <param name="fragment_type" value="full"/>
      <param name="separator" value=","/>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="charge" value="1 2 3"/>
      <param name="format" value="list"/>
      <param name="average_mass" value="false"/>
      <param name="fragment_type" value="full"/>
      <param name="separator" value=""/>

        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_MetaboliteAdductDecharger">
    <test expect_num_outputs="2">
      <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="MetaboliteAdductDecharger_input.featureXML"/>
      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="MetaboliteFeatureDeconvolution">
          <param name="charge_min" value="1"/>
          <param name="charge_max" value="3"/>
          <param name="charge_span_max" value="3"/>
          <param name="q_try" value="feature"/>
          <param name="retention_max_diff" value="1.0"/>
          <param name="retention_max_diff_local" value="1.0"/>
          <param name="mass_max_diff" value="0.05"/>
          <param name="unit" value="Da"/>
          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
          <param name="max_neutrals" value="1"/>
          <param name="use_minority_bound" value="true"/>
          <param name="max_minority_bound" value="3"/>
          <param name="min_rt_overlap" value="0.66"/>
          <param name="intensity_filter" value="false"/>
          <param name="negative_mode" value="false"/>
          <param name="default_map_label" value="decharged features"/>
          <param name="verbose_level" value="0"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <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="MetaboliteAdductDecharger_input.featureXML"/>
      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <section name="MetaboliteFeatureDeconvolution">
          <param name="charge_min" value="1"/>
          <param name="charge_max" value="3"/>
          <param name="charge_span_max" value="3"/>
          <param name="q_try" value="feature"/>
          <param name="retention_max_diff" value="1.0"/>
          <param name="retention_max_diff_local" value="1.0"/>
          <param name="mass_max_diff" value="0.05"/>
          <param name="unit" value="Da"/>
          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
          <param name="max_neutrals" value="1"/>
          <param name="use_minority_bound" value="true"/>
          <param name="max_minority_bound" value="3"/>
          <param name="min_rt_overlap" value="0.66"/>
          <param name="intensity_filter" value="false"/>
          <param name="negative_mode" value="false"/>
          <param name="default_map_label" value="decharged features"/>
          <param name="verbose_level" value="0"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_MetaboliteSpectralMatcher">
</xml>
  <xml name="autotest_MetaProSIP">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">

  <xml name="autotest_MSFraggerAdapter"/>
  <xml name="autotest_MSGFPlusAdapter">
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="add_decoys" value="false"/>
        <param name="legacy_conversion" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="spectra.mzML"/>
      <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
      <param name="database" value="proteins.fasta"/>
      <param name="precursor_mass_tolerance" value="10.0"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="isotope_error_range" value="0,1"/>
      <param name="fragment_method" value="from_spectrum"/>
      <param name="instrument" value="high_res"/>

      <param name="min_peptide_length" value="6"/>
      <param name="max_peptide_length" value="40"/>
      <param name="matches_per_spec" value="1"/>
      <param name="add_features" value="false"/>
      <param name="max_mods" value="2"/>
      <param name="max_missed_cleavages" value="-1"/>
      <param name="tasks" value="0"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value="Oxidation (M)"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MzTabExporter_3_input.featureXML"/>
      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="first_run_inference_only" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="Epifany_2_out.consensusXML"/>
      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="first_run_inference_only" value="true"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="first_run_inference_only" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MzTabExporter_6_input.idXML"/>
      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="first_run_inference_only" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="opt_columns" value="subfeatures"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_OpenSwathDIAPreScoring">
</xml>
  <xml name="autotest_OpenSwathFeatureXMLToTSV">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

        <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="-1.0"/>
          <param name="peak_integration" value="original"/>

    <test expect_num_outputs="4">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="false"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="false"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
      <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
      <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cache"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cacheWorkingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="true"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
      <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="false"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="550.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
      <param name="tr_type" value=""/>
      <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
      <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="true"/>
      <param name="rt_extraction_window" value="-1.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.2"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="none"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <param name="use_dia_scores" value="true"/>
          <param name="use_ms1_correlation" value="false"/>
          <param name="use_sonar_scores" value="true"/>
          <param name="use_ion_mobility_scores" value="false"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
      <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="sqMass"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
      <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="2"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="true"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="2"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="cache"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_ms1_fullscan" value="false"/>
          <param name="use_ms1_mi" value="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="false"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
      <param name="tr_type" value="pqp"/>
      <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="0.05"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <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="11"/>
            <param name="sgolay_polynomial_order" value="3"/>
            <param name="gauss_width" value="30.0"/>
            <param name="use_gauss" value="false"/>
            <param name="peak_width" value="-1.0"/>
            <param name="signal_to_noise" value="0.1"/>
            <param name="write_sn_log_messages" value="false"/>
            <param name="remove_overlapping_peaks" value="true"/>
            <param name="method" value="corrected"/>
          </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="max_iteration" value="10"/>
        </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_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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>
      </section>
      <section name="Library">
        <param name="retentionTimeInterpretation" value="iRT"/>
        <param name="override_group_label_check" value="false"/>
        <param name="force_invalid_mods" value="false"/>
      </section>
      <section name="RTNormalization">
        <param name="alignmentMethod" value="linear"/>
        <param name="outlierMethod" value="iter_residual"/>
        <param name="useIterativeChauvenet" value="false"/>
        <param name="RANSACMaxIterations" value="1000"/>
        <param name="RANSACMaxPercentRTThreshold" value="3"/>
        <param name="RANSACSamplingSize" value="10"/>
        <param name="estimateBestPeptides" value="false"/>
        <param name="InitialQualityCutoff" value="0.5"/>
        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>
      <section name="Scoring">
        <param name="stop_report_after_feature" value="5"/>
        <param name="rt_normalization_factor" value="100.0"/>
        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <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="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <param name="use_rt_score" value="true"/>
          <param name="use_library_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="true"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="4">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="Th"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="false"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="normal"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
      <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="0.05"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>
        <param name="debug_im_file" value=""/>
        <param name="debug_mz_file" value=""/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.6666666666666666"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>

          <param name="use_rt_score" value="true"/>
          <param name="use_library_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="true"/>
          <param name="use_sn_score" value="true"/>
          <param name="use_mi_score" value="true"/>
          <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"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="3">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="sort_swath_maps" value="false"/>
        <param name="enable_ms1" value="true"/>
        <param name="enable_ipf" value="true"/>
        <param name="out_chrom_type" value="mzML"/>
        <param name="min_upper_edge_dist" value="0.0"/>
        <param name="extra_rt_extraction_window" value="0.0"/>
        <param name="mz_extraction_window_unit" value="ppm"/>
        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
        <param name="use_ms1_ion_mobility" value="true"/>
        <param name="matching_window_only" value="true"/>
        <param name="irt_mz_extraction_window" value="50.0"/>
        <param name="irt_mz_extraction_window_unit" value="ppm"/>
        <param name="irt_im_extraction_window" value="-1.0"/>
        <param name="min_rsq" value="0.95"/>
        <param name="min_coverage" value="0.6"/>
        <param name="split_file_input" value="false"/>
        <param name="use_elution_model_score" value="false"/>
        <param name="readOptions" value="workingInMemory"/>
        <param name="mz_correction_function" value="none"/>
        <param name="extraction_function" value="tophat"/>
        <param name="batchSize" value="1000"/>
        <param name="ms1_isotopes" value="3"/>
        <param name="force" value="false"/>
        <param name="test" value="false"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
      <param name="tr_type" value=""/>
      <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="sonar" value="false"/>
      <param name="rt_extraction_window" value="600.0"/>
      <param name="ion_mobility_window" value="-1.0"/>
      <param name="mz_extraction_window" value="50.0"/>
      <param name="mz_extraction_window_ms1" value="50.0"/>
      <param name="im_extraction_window_ms1" value="-1.0"/>
      <section name="Debugging"/>
      <section name="Calibration">
        <param name="ms1_im_calibration" value="false"/>
        <param name="im_correction_function" value="linear"/>

        <param name="OverallQualityCutoff" value="5.5"/>
        <param name="NrRTBins" value="10"/>
        <param name="MinPeptidesPerBin" value="1"/>
        <param name="MinBinsFilled" value="8"/>
        <section name="lowess">
          <param name="span" value="0.05"/>
        </section>
        <section name="b_spline">
          <param name="num_nodes" value="5"/>
        </section>
      </section>

        <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="min_peak_width" value="-1.0"/>
          <param name="peak_integration" value="original"/>
          <param name="background_subtraction" value="none"/>
          <param name="recalculate_peaks" value="true"/>
          <param name="use_precursors" value="false"/>
          <param name="use_consensus" value="true"/>
          <param name="recalculate_peaks_max_z" value="0.75"/>
          <param name="minimal_quality" value="-1.5"/>
          <param name="resample_boundary" value="15.0"/>
          <param name="compute_peak_quality" value="false"/>

          <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="true"/>
          <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="true"/>
          <param name="use_uis_scores" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>

        <param name="processOption" value="inmemory"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="PeakPickerHiRes_input.mzML"/>
      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <param name="signal_to_noise" value="1.0"/>
        <param name="spacing_difference_gap" value="4.0"/>
        <param name="spacing_difference" value="1.5"/>
        <param name="missing" value="1"/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="true"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="0"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="3"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="full"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="semi"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="remove"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="error"/>
      <param name="aaa_max" value="3"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="true"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="auto"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="warn"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="false"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="error"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="auto"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>

      <param name="decoy_string_position" value="prefix"/>
      <param name="missing_decoy_action" value="error"/>
      <param name="write_protein_sequence" value="true"/>
      <param name="write_protein_description" value="false"/>
      <param name="keep_unreferenced_proteins" value="false"/>
      <param name="unmatched_action" value="error"/>
      <param name="aaa_max" value="4"/>
      <param name="mismatches_max" value="0"/>
      <param name="IL_equivalent" value="false"/>
      <section name="enzyme">
        <param name="name" value="auto"/>
        <param name="specificity" value="none"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.5"/>
        <param name="trainFDR" value="0.5"/>
        <param name="maxiter" value="10"/>
        <param name="nested_xval_bins" value="1"/>
        <param name="quick_validation" value="false"/>
        <param name="static" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="nested_xval_bins" value="1"/>
        <param name="quick_validation" value="false"/>
        <param name="static" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="nested_xval_bins" value="1"/>
        <param name="quick_validation" value="false"/>
        <param name="static" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.01"/>
        <param name="trainFDR" value="0.01"/>
        <param name="maxiter" value="10"/>
        <param name="nested_xval_bins" value="1"/>
        <param name="quick_validation" value="false"/>
        <param name="static" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

        <param name="cpos" value="0.0"/>
        <param name="cneg" value="0.0"/>
        <param name="testFDR" value="0.5"/>
        <param name="trainFDR" value="0.5"/>
        <param name="maxiter" value="10"/>
        <param name="nested_xval_bins" value="1"/>
        <param name="quick_validation" value="false"/>
        <param name="static" value="false"/>
        <param name="default_direction" value=""/>
        <param name="verbose" value="2"/>
        <param name="unitnorm" value="false"/>
        <param name="test_each_iteration" value="false"/>
        <param name="override" value="false"/>

      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="merge_runs" value="all"/>
      <param name="annotate_indist_groups" value="true"/>
      <section name="Merging">
        <param name="annotate_origin" value="false"/>
        <param name="allow_disagreeing_settings" value="false"/>
      </section>
      <section name="Algorithm">
        <param name="min_peptides_per_protein" value="1"/>
        <param name="score_aggregation_method" value="maximum"/>
        <param name="treat_charge_variants_separately" value="true"/>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <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="ProteinQuantifier_input.consensusXML"/>
      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="top" value="3"/>
      <param name="average" value="sum"/>
      <param name="include_all" value="true"/>
      <param name="best_charge_and_fraction" value="false"/>
      <param name="greedy_group_resolution" value="false"/>

      <section name="format">
        <param name="separator" value=""/>
        <param name="quoting" value="double"/>
        <param name="replacement" value="_"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      <section name="FragmentMassError">
        <param name="unit" value="auto"/>
        <param name="tolerance" value="20.0"/>
      </section>
      <section name="MS2_id_rate">
        <param name="assume_all_target" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

      <param name="in" value="SimpleSearchEngine_1.mzML"/>
      <param name="database" value="SimpleSearchEngine_1.fasta"/>
      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <section name="Search">
        <param name="enzyme" value="Trypsin"/>
        <param name="decoys" value="false"/>
        <section name="precursor">
          <param name="mass_tolerance" value="5.0"/>
          <param name="mass_tolerance_unit" value="ppm"/>
          <param name="min_charge" value="2"/>
          <param name="max_charge" value="5"/>

        </section>
        <section name="modifications">
          <param name="fixed" value=""/>
          <param name="variable" value="Oxidation (M)"/>
          <param name="variable_max_per_peptide" value="2"/>
        </section>
        <section name="annotate">
          <param name="PSM" value=""/>
        </section>
        <section name="peptide">
          <param name="min_size" value="7"/>
          <param name="max_size" value="40"/>
          <param name="missed_cleavages" value="1"/>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

        <param name="no_masstrace_info_isotope_pattern" value="false"/>
      </section>
      <section name="sirius">
        <param name="profile" value="qtof"/>
        <param name="candidates" value="5"/>
        <param name="database" value="pubchem"/>
        <param name="noise" value="0"/>
        <param name="ppm_max" value="10"/>
        <param name="isotope" value="both"/>
        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
        <param name="compound_timeout" value="10"/>
        <param name="tree_timeout" value="0"/>
        <param name="top_n_hits" value="10"/>
        <param name="auto_charge" value="true"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" value="false"/>
      </section>

    </test>
  </xml>
  <xml name="autotest_SpectraMerger">
</xml>
  <xml name="autotest_SpectraSTSearchAdapter"/>
  <xml name="autotest_StaticModification">
</xml>
  <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
</xml>
  <xml name="autotest_TargetedFileConverter">
    <test expect_num_outputs="2">
      <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="TextExporter_1_input.featureXML"/>
      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_2_input.consensusXML"/>
      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

        <param name="sort_by_size" value="true"/>
      </section>
      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_3_input.idXML"/>
      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_3_input.idXML"/>
      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_5_input.idXML"/>
      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_6_input.featureXML"/>
      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_7_input.consensusXML"/>
      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="RT_then_MZ"/>
        <param name="sort_by_maps" value="true"/>
        <param name="sort_by_size" value="true"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_1_input.featureXML"/>
      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="true"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TextExporter_9_input.idXML"/>
      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="separator" value=""/>
      <param name="replacement" value="_"/>
      <param name="quoting" value="none"/>
      <param name="no_ids" value="false"/>
      <section name="feature">

      <section name="consensus">
        <param name="sorting_method" value="none"/>
        <param name="sort_by_maps" value="false"/>
        <param name="sort_by_size" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>

        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TOFCalibration_1_input.mzML"/>
      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
      <param name="peak_data" value="false"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>

        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="TOFCalibration_2_input.mzML"/>
      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
      <param name="peak_data" value="true"/>
      <section name="algorithm">
        <section name="PeakPicker">
          <param name="signal_to_noise" value="3.0"/>
          <param name="centroid_percentage" value="0.6"/>

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <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="spectra.mzML"/>
      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="proteinslong.fasta"/>
      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
      <param name="ignore_adapter_param" value="false"/>
      <param name="precursor_mass_tolerance" value="5.0"/>
      <param name="fragment_mass_tolerance" value="0.3"/>
      <param name="precursor_error_units" value="ppm"/>
      <param name="fragment_error_units" value="Da"/>
      <param name="max_precursor_charge" value="0"/>
      <param name="no_isotope_error" value="false"/>
      <param name="fixed_modifications" value=""/>
      <param name="variable_modifications" value="Oxidation (M)"/>
      <param name="minimum_fragment_mz" value="150.0"/>
      <param name="enzyme" value="Trypsin"/>
      <param name="missed_cleavages" value="1"/>
      <param name="semi_cleavage" value="false"/>
      <param name="output_results" value="all"/>
      <param name="max_valid_expect" value="0.1"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>