view macros_autotest.xml @ 12:f918cb7aefd5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:27:04 +0000
parents 65be0674bb70
children 31bc4129f589
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<?xml version='1.0' encoding='UTF-8'?>
<macros>
  <xml name="autotest_AccurateMassSearch">
    <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="ConsensusMapNormalizer_input.consensusXML"/>
      <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
      <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
      <section name="db">
        <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
        <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
      </section>
      <section name="algorithm">
        <param name="mass_error_value" value="5.0"/>
        <param name="mass_error_unit" value="ppm"/>
        <param name="ionization_mode" value="positive"/>
        <param name="isotopic_similarity" value="false"/>
        <param name="use_feature_adducts" value="false"/>
        <param name="keep_unidentified_masses" value="false"/>
        <section name="mzTab">
          <param name="exportIsotopeIntensities" value="false"/>
        </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="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="AccurateMassSearch_2_input.featureXML"/>
      <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
      <section name="db">
        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
      </section>
      <section name="algorithm">
        <param name="mass_error_value" value="5.0"/>
        <param name="mass_error_unit" value="ppm"/>
        <param name="ionization_mode" value="positive"/>
        <param name="isotopic_similarity" value="false"/>
        <param name="use_feature_adducts" value="false"/>
        <param name="keep_unidentified_masses" value="false"/>
        <section name="mzTab">
          <param name="exportIsotopeIntensities" value="true"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_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="AccurateMassSearch_2_input.featureXML"/>
      <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
      <section name="db">
        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
      </section>
      <section name="algorithm">
        <param name="mass_error_value" value="5.0"/>
        <param name="mass_error_unit" value="ppm"/>
        <param name="ionization_mode" value="positive"/>
        <param name="isotopic_similarity" value="false"/>
        <param name="use_feature_adducts" value="false"/>
        <param name="keep_unidentified_masses" value="false"/>
        <section name="mzTab">
          <param name="exportIsotopeIntensities" value="false"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_AssayGeneratorMetabo">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="none"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="false"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="1"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="5.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="0.005"/>
        <param name="precursor_mz_tolerance_unit" value="Da"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="false"/>
        <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="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="none"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="false"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="1"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="5.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="0.005"/>
        <param name="precursor_mz_tolerance_unit" value="Da"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="false"/>
        <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="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="none"/>
      <param name="method" value="consensus_spectrum"/>
      <param name="use_exact_mass" value="false"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="1"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="5.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="0.005"/>
        <param name="precursor_mz_tolerance_unit" value="Da"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="false"/>
        <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="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="none"/>
      <param name="method" value="consensus_spectrum"/>
      <param name="use_exact_mass" value="false"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="1"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="5.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="0.005"/>
        <param name="precursor_mz_tolerance_unit" value="Da"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="false"/>
        <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="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="none"/>
      <param name="method" value="consensus_spectrum"/>
      <param name="use_exact_mass" value="false"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="true"/>
      <param name="min_transitions" value="1"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="5.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="0.005"/>
        <param name="precursor_mz_tolerance_unit" value="Da"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="false"/>
        <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="false"/>
        <param name="ion_tree" value="false"/>
        <param name="no_recalibration" value="false"/>
        <param name="most_intense_ms2" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="sirius"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="true"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="2"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="3.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="10.0"/>
        <param name="precursor_mz_tolerance_unit" value="ppm"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="true"/>
        <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="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="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="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="sirius"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="true"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="true"/>
      <param name="min_transitions" value="2"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="3.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="10.0"/>
        <param name="precursor_mz_tolerance_unit" value="ppm"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="true"/>
        <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="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="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="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="0.0"/>
        <param name="max_fragment_mz" value="2000.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="sirius"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="true"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="2"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="3.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="10.0"/>
        <param name="precursor_mz_tolerance_unit" value="ppm"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="true"/>
        <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="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="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="precursor_recalibration_window" value="0.1"/>
        <param name="precursor_recalibration_window_unit" value="Da"/>
        <param name="min_fragment_mz" value="100.0"/>
        <param name="max_fragment_mz" value="900.0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
      <param name="out_type" value="tsv"/>
      <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
      <param name="fragment_annotation" value="sirius"/>
      <param name="method" value="highest_intensity"/>
      <param name="use_exact_mass" value="true"/>
      <param name="exclude_ms2_precursor" value="false"/>
      <param name="precursor_mz_distance" value="0.0001"/>
      <param name="precursor_rt_tolerance" value="5.0"/>
      <param name="use_known_unknowns" value="false"/>
      <param name="min_transitions" value="2"/>
      <param name="max_transitions" value="3"/>
      <param name="cosine_similarity_threshold" value="0.98"/>
      <param name="transition_threshold" value="3.0"/>
      <param name="out_workspace_directory" value=""/>
      <section name="deisotoping">
        <param name="use_deisotoper" value="false"/>
        <param name="fragment_tolerance" value="1.0"/>
        <param name="fragment_unit" value="ppm"/>
        <param name="min_charge" value="1"/>
        <param name="max_charge" value="1"/>
        <param name="min_isopeaks" value="2"/>
        <param name="max_isopeaks" value="3"/>
        <param name="keep_only_deisotoped" value="false"/>
        <param name="annotate_charge" value="false"/>
      </section>
      <section name="preprocessing">
        <param name="filter_by_num_masstraces" value="1"/>
        <param name="precursor_mz_tolerance" value="10.0"/>
        <param name="precursor_mz_tolerance_unit" value="ppm"/>
        <param name="precursor_rt_tolerance" value="5"/>
        <param name="isotope_pattern_iterations" value="3"/>
        <param name="feature_only" value="true"/>
        <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="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="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_BaselineFilter">
    <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="BaselineFilter_input.mzML"/>
      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="struc_elem_length" value="1.5"/>
      <param name="struc_elem_unit" value="Thomson"/>
      <param name="method" value="tophat"/>
      <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_ClusterMassTracesByPrecursor">
</xml>
  <xml name="autotest_ClusterMassTraces">
</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="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="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="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="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="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="CometAdapter_3.mzML"/>
      <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <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>
    </test>
  </xml>
  <xml name="autotest_CompNovoCID">
    <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="CompNovoCID_1_input.mzML"/>
      <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <section name="algorithm">
        <param name="max_number_aa_per_decomp" value="4"/>
        <param name="tryptic_only" value="true"/>
        <param name="precursor_mass_tolerance" value="0.3"/>
        <param name="fragment_mass_tolerance" value="0.3"/>
        <param name="max_number_pivot" value="9"/>
        <param name="max_subscore_number" value="40"/>
        <param name="decomp_weights_precision" value="0.01"/>
        <param name="double_charged_iso_threshold" value="0.6"/>
        <param name="max_mz" value="2000.0"/>
        <param name="min_mz" value="200.0"/>
        <param name="max_isotope_to_score" value="3"/>
        <param name="max_decomp_weight" value="450.0"/>
        <param name="max_isotope" value="3"/>
        <param name="missed_cleavages" value="1"/>
        <param name="number_of_hits" value="1"/>
        <param name="estimate_precursor_mz" value="true"/>
        <param name="number_of_prescoring_hits" value="250"/>
        <param name="fixed_modifications" value=""/>
        <param name="variable_modifications" value=""/>
        <param name="residue_set" value="Natural19WithoutI"/>
      </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_CompNovo">
    <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="CompNovo_1_input.mzML"/>
      <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <section name="algorithm">
        <param name="max_number_aa_per_decomp" value="4"/>
        <param name="tryptic_only" value="true"/>
        <param name="precursor_mass_tolerance" value="0.3"/>
        <param name="fragment_mass_tolerance" value="0.3"/>
        <param name="max_number_pivot" value="9"/>
        <param name="max_subscore_number" value="40"/>
        <param name="decomp_weights_precision" value="0.01"/>
        <param name="double_charged_iso_threshold" value="0.6"/>
        <param name="max_mz" value="2000.0"/>
        <param name="min_mz" value="200.0"/>
        <param name="max_isotope_to_score" value="3"/>
        <param name="max_decomp_weight" value="450.0"/>
        <param name="max_isotope" value="3"/>
        <param name="missed_cleavages" value="1"/>
        <param name="number_of_hits" value="1"/>
        <param name="estimate_precursor_mz" value="true"/>
        <param name="number_of_prescoring_hits" value="250"/>
        <param name="fixed_modifications" value=""/>
        <param name="variable_modifications" value=""/>
        <param name="residue_set" value="Natural19WithoutI"/>
      </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_ConsensusID">
    <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_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>
      <section name="PEPMatrix">
        <param name="matrix" value="PAM30MS"/>
        <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_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>
      <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_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>
      <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_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>
      <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_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>
      <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_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>
      <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>
  </xml>
  <xml name="autotest_ConsensusMapNormalizer">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="accession_filter" value=""/>
        <param name="description_filter" value=""/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
      <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="algorithm_type" value="robust_regression"/>
      <param name="ratio_threshold" value="0.67"/>
      <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_CruxAdapter">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="custom_enzyme" value=""/>
        <param name="decoy_prefix" value="decoy_"/>
        <param name="deisotope" value="false"/>
        <param name="report_decoys" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="spectra_comet.mzML"/>
      <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="database" value="proteins.fasta"/>
      <param name="extra_index_args" value=""/>
      <param name="extra_search_args" value=""/>
      <param name="extra_percolator_args" value=""/>
      <param name="precursor_mass_tolerance" value="10.0"/>
      <param name="precursor_mass_units" value="ppm"/>
      <param name="fragment_bin_offset" value="0.0"/>
      <param name="fragment_bin_width" value="0.02"/>
      <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="train_fdr" value="0.01"/>
      <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_CVInspector">
</xml>
  <xml name="autotest_DatabaseFilter">
    <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="DatabaseFilter_1.fasta"/>
      <param name="id" value="DatabaseFilter_1.idXML"/>
      <param name="method" value="whitelist"/>
      <output name="out" file="DatabaseFilter_1_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>
    <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="DatabaseFilter_1.fasta"/>
      <param name="id" value="DatabaseFilter_1.idXML"/>
      <param name="method" value="blacklist"/>
      <output name="out" file="DatabaseFilter_2_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>
    <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="DatabaseFilter_3.fasta"/>
      <param name="id" value="DatabaseFilter_3.mzid"/>
      <param name="method" value="whitelist"/>
      <output name="out" file="DatabaseFilter_3_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>
    <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="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_Decharger">
    <test expect_num_outputs="4">
      <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="Decharger_input.featureXML"/>
      <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <section name="FeatureDeconvolution">
          <param name="charge_min" value="1"/>
          <param name="charge_max" value="10"/>
          <param name="charge_span_max" value="4"/>
          <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="0.1"/>
          <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
          <param name="max_neutrals" value="0"/>
          <param name="max_minority_bound" value="2"/>
          <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,outpairs_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </xml>
  <xml name="autotest_DecoyDatabase">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="seed" value="1"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="DecoyDatabase_1.fasta"/>
      <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="decoy_string" value="DECOY_"/>
      <param name="decoy_string_position" value="prefix"/>
      <param name="only_decoy" value="true"/>
      <param name="type" value="protein"/>
      <param name="method" value="reverse"/>
      <param name="enzyme" value="Trypsin"/>
      <section name="Decoy">
        <param name="non_shuffle_pattern" value=""/>
        <param name="keepPeptideNTerm" value="true"/>
        <param name="keepPeptideCTerm" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="seed" value="42"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="DecoyDatabase_1.fasta"/>
      <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="decoy_string" value="blabla"/>
      <param name="decoy_string_position" value="prefix"/>
      <param name="only_decoy" value="false"/>
      <param name="type" value="protein"/>
      <param name="method" value="shuffle"/>
      <param name="enzyme" value="Trypsin"/>
      <section name="Decoy">
        <param name="non_shuffle_pattern" value="KRP"/>
        <param name="keepPeptideNTerm" value="true"/>
        <param name="keepPeptideCTerm" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="seed" value="42"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="DecoyDatabase_1.fasta"/>
      <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="decoy_string" value="blabla"/>
      <param name="decoy_string_position" value="prefix"/>
      <param name="only_decoy" value="false"/>
      <param name="type" value="protein"/>
      <param name="method" value="shuffle"/>
      <param name="enzyme" value="Chymotrypsin"/>
      <section name="Decoy">
        <param name="non_shuffle_pattern" value="KR"/>
        <param name="keepPeptideNTerm" value="true"/>
        <param name="keepPeptideCTerm" 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>
    </test>
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="shuffle_max_attempts" value="30"/>
        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
        <param name="seed" value="42"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="DecoyDatabase_4.fasta"/>
      <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
      <param name="decoy_string" value="blabla"/>
      <param name="decoy_string_position" value="prefix"/>
      <param name="only_decoy" value="false"/>
      <param name="type" value="RNA"/>
      <param name="method" value="reverse"/>
      <param name="enzyme" value="Trypsin"/>
      <section name="Decoy">
        <param name="non_shuffle_pattern" value=""/>
        <param name="keepPeptideNTerm" value="true"/>
        <param name="keepPeptideCTerm" 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>
    </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="adv_opts_selector" value="advanced"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="DTAExtractor_1_input.mzML"/>
      <param name="out" value="DTAExtractor"/>
      <param name="mz" value=":"/>
      <param name="rt" value=":61"/>
      <param name="level" value="1,2,3"/>
      <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="1">
      <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="DTAExtractor_1_input.mzML"/>
      <param name="out" value="DTAExtractor"/>
      <param name="mz" value=":"/>
      <param name="rt" value=":"/>
      <param name="level" value="1"/>
      <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="1">
      <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="DTAExtractor_1_input.mzML"/>
      <param name="out" value="DTAExtractor"/>
      <param name="mz" value=":1000"/>
      <param name="rt" value=":"/>
      <param name="level" value="2"/>
      <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_EICExtractor">
</xml>
  <xml name="autotest_Epifany">
    <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="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="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"/>
        </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_ERPairFinder">
</xml>
  <xml name="autotest_ExternalCalibration">
    <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="ExternalCalibration_1_input.mzML"/>
      <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="offset" value="-5.5"/>
      <param name="slope" value="0.0001"/>
      <param name="power" value="0.0"/>
      <param name="ms_level" value="1"/>
      <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="ExternalCalibration_1_input.mzML"/>
      <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="offset" value="-5.5"/>
      <param name="slope" value="0.0001"/>
      <param name="power" value="0.0"/>
      <param name="ms_level" value="2"/>
      <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_FalseDiscoveryRate">
    <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="FalseDiscoveryRate_OMSSA.idXML"/>
      <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="true"/>
      <param name="protein" value="false"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="false"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </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="FalseDiscoveryRate_OMSSA.idXML"/>
      <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="true"/>
      <param name="protein" value="false"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="false"/>
        <param name="treat_runs_separately" value="true"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </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="FalseDiscoveryRate_OMSSA.idXML"/>
      <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="true"/>
      <param name="protein" value="false"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="true"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </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="FalseDiscoveryRate_OMSSA_4.idXML"/>
      <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="true"/>
      <param name="protein" value="false"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="true"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </test>
    <test expect_num_outputs="2">
      <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="FalseDiscoveryRate_5_input.idXML"/>
      <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="false"/>
      <param name="protein" value="true"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="false"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="true"/>
        <param name="conservative" 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>
    </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="FalseDiscoveryRate_6_input.idXML"/>
      <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="true"/>
      <param name="protein" value="false"/>
      <section name="FDR">
        <param name="PSM" value="0.05"/>
        <param name="protein" value="1.0"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="false"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </test>
    <test expect_num_outputs="2">
      <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="FalseDiscoveryRate_7_input.idXML"/>
      <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="PSM" value="false"/>
      <param name="protein" value="true"/>
      <section name="FDR">
        <param name="PSM" value="1.0"/>
        <param name="protein" value="0.3"/>
        <section name="cleanup">
          <param name="remove_proteins_without_psms" value="true"/>
          <param name="remove_psms_without_proteins" value="true"/>
          <param name="remove_spectra_without_psms" value="true"/>
        </section>
      </section>
      <section name="algorithm">
        <param name="no_qvalues" value="false"/>
        <param name="use_all_hits" value="false"/>
        <param name="split_charge_variants" value="false"/>
        <param name="treat_runs_separately" value="false"/>
        <param name="add_decoy_peptides" value="false"/>
        <param name="add_decoy_proteins" value="false"/>
        <param name="conservative" 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>
    </test>
  </xml>
  <xml name="autotest_FeatureFinderCentroided">
    <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"/>
        <param name="pseudo_rt_shift" value="500.0"/>
      </conditional>
      <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
      <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="intensity">
          <param name="bins" value="1"/>
        </section>
        <section name="mass_trace">
          <param name="mz_tolerance" value="0.02"/>
          <param name="min_spectra" value="14"/>
          <param name="max_missing" value="1"/>
          <param name="slope_bound" value="0.1"/>
        </section>
        <section name="isotopic_pattern">
          <param name="charge_low" value="2"/>
          <param name="charge_high" value="2"/>
          <param name="mz_tolerance" value="0.02"/>
          <param name="intensity_percentage" value="10.0"/>
          <param name="intensity_percentage_optional" value="0.1"/>
          <param name="optional_fit_improvement" value="2.0"/>
          <param name="mass_window_width" value="100.0"/>
          <param name="abundance_12C" value="98.93"/>
          <param name="abundance_14N" value="99.632"/>
        </section>
        <section name="seed">
          <param name="min_score" value="0.8"/>
        </section>
        <section name="fit">
          <param name="max_iterations" value="500"/>
        </section>
        <section name="feature">
          <param name="min_score" value="0.7"/>
          <param name="min_isotope_fit" value="0.8"/>
          <param name="min_trace_score" value="0.5"/>
          <param name="min_rt_span" value="0.333"/>
          <param name="max_rt_span" value="2.5"/>
          <param name="rt_shape" value="symmetric"/>
          <param name="max_intersection" value="0.35"/>
          <param name="reported_mz" value="monoisotopic"/>
        </section>
        <section name="user-seed">
          <param name="rt_tolerance" value="5.0"/>
          <param name="mz_tolerance" value="1.1"/>
          <param name="min_score" value="0.5"/>
        </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_FeatureFinderIdentification">
    <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="1000"/>
        <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>
      </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_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="extract">
        <param name="batch_size" value="1000"/>
        <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="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>
      </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_FeatureFinderIsotopeWavelet">
</xml>
  <xml name="autotest_FeatureFinderMetaboIdent">
    <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="FeatureFinderMetaboIdent_1_input.mzML"/>
      <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
      <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="extract">
        <param name="mz_window" value="5.0"/>
        <param name="n_isotopes" value="2"/>
        <param name="isotope_pmin" value="0.0"/>
        <param name="rt_window" value="20.0"/>
      </section>
      <section name="detect">
        <param name="peak_width" value="3.0"/>
        <param name="min_peak_width" value="0.2"/>
        <param name="signal_to_noise" value="0.8"/>
      </section>
      <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>
  </xml>
  <xml name="autotest_FeatureFinderMetabo">
    <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="FeatureFinderMetabo_1_input.mzML"/>
      <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="common">
          <param name="noise_threshold_int" value="10.0"/>
          <param name="chrom_peak_snr" value="3.0"/>
          <param name="chrom_fwhm" value="5.0"/>
        </section>
        <section name="mtd">
          <param name="mass_error_ppm" value="20.0"/>
          <param name="reestimate_mt_sd" value="true"/>
          <param name="quant_method" value="area"/>
          <param name="trace_termination_criterion" value="outlier"/>
          <param name="trace_termination_outliers" value="5"/>
          <param name="min_sample_rate" value="0.5"/>
          <param name="min_trace_length" value="5.0"/>
          <param name="max_trace_length" value="300.0"/>
        </section>
        <section name="epd">
          <param name="enabled" value="true"/>
          <param name="width_filtering" value="off"/>
          <param name="min_fwhm" value="3.0"/>
          <param name="max_fwhm" value="60.0"/>
          <param name="masstrace_snr_filtering" value="false"/>
        </section>
        <section name="ffm">
          <param name="local_rt_range" value="10.0"/>
          <param name="local_mz_range" value="6.5"/>
          <param name="charge_lower_bound" value="1"/>
          <param name="charge_upper_bound" value="3"/>
          <param name="report_summed_ints" value="false"/>
          <param name="enable_RT_filtering" value="true"/>
          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
          <param name="mz_scoring_13C" value="true"/>
          <param name="use_smoothed_intensities" value="true"/>
          <param name="report_convex_hulls" value="false"/>
          <param name="remove_single_traces" value="false"/>
          <param name="mz_scoring_by_elements" value="false"/>
          <param name="elements" value="CHNOPS"/>
        </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="FeatureFinderMetabo_2_input.mzML"/>
      <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="common">
          <param name="noise_threshold_int" value="100.0"/>
          <param name="chrom_peak_snr" value="0.0"/>
          <param name="chrom_fwhm" value="100.0"/>
        </section>
        <section name="mtd">
          <param name="mass_error_ppm" value="5.0"/>
          <param name="reestimate_mt_sd" value="true"/>
          <param name="quant_method" value="median"/>
          <param name="trace_termination_criterion" value="sample_rate"/>
          <param name="trace_termination_outliers" value="2"/>
          <param name="min_sample_rate" value="0.01"/>
          <param name="min_trace_length" value="30.0"/>
          <param name="max_trace_length" value="3000.0"/>
        </section>
        <section name="epd">
          <param name="enabled" value="false"/>
          <param name="width_filtering" value="off"/>
          <param name="min_fwhm" value="10.0"/>
          <param name="max_fwhm" value="80.0"/>
          <param name="masstrace_snr_filtering" value="false"/>
        </section>
        <section name="ffm">
          <param name="local_rt_range" value="10.0"/>
          <param name="local_mz_range" value="4.5"/>
          <param name="charge_lower_bound" value="1"/>
          <param name="charge_upper_bound" value="3"/>
          <param name="report_summed_ints" value="false"/>
          <param name="enable_RT_filtering" value="false"/>
          <param name="isotope_filtering_model" value="none"/>
          <param name="mz_scoring_13C" value="false"/>
          <param name="use_smoothed_intensities" value="false"/>
          <param name="report_convex_hulls" value="true"/>
          <param name="remove_single_traces" value="false"/>
          <param name="mz_scoring_by_elements" value="false"/>
          <param name="elements" value="CHNOPS"/>
        </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="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="FeatureFinderMetabo_3_input.mzML"/>
      <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <section name="common">
          <param name="noise_threshold_int" value="10.0"/>
          <param name="chrom_peak_snr" value="3.0"/>
          <param name="chrom_fwhm" value="5.0"/>
        </section>
        <section name="mtd">
          <param name="mass_error_ppm" value="5.0"/>
          <param name="reestimate_mt_sd" value="true"/>
          <param name="quant_method" value="area"/>
          <param name="trace_termination_criterion" value="outlier"/>
          <param name="trace_termination_outliers" value="5"/>
          <param name="min_sample_rate" value="0.5"/>
          <param name="min_trace_length" value="5.0"/>
          <param name="max_trace_length" value="-1.0"/>
        </section>
        <section name="epd">
          <param name="enabled" value="true"/>
          <param name="width_filtering" value="fixed"/>
          <param name="min_fwhm" value="3.0"/>
          <param name="max_fwhm" value="60.0"/>
          <param name="masstrace_snr_filtering" value="false"/>
        </section>
        <section name="ffm">
          <param name="local_rt_range" value="10.0"/>
          <param name="local_mz_range" value="6.5"/>
          <param name="charge_lower_bound" value="1"/>
          <param name="charge_upper_bound" value="3"/>
          <param name="report_summed_ints" value="false"/>
          <param name="enable_RT_filtering" value="true"/>
          <param name="isotope_filtering_model" value="none"/>
          <param name="mz_scoring_13C" value="true"/>
          <param name="use_smoothed_intensities" value="true"/>
          <param name="report_convex_hulls" value="true"/>
          <param name="remove_single_traces" value="false"/>
          <param name="mz_scoring_by_elements" value="false"/>
          <param name="elements" value="CHNOPS"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_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="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
      <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <section name="algorithm">
        <section name="common">
          <param name="noise_threshold_int" value="10.0"/>
          <param name="chrom_peak_snr" value="3.0"/>
          <param name="chrom_fwhm" value="5.0"/>
        </section>
        <section name="mtd">
          <param name="mass_error_ppm" value="5.0"/>
          <param name="reestimate_mt_sd" value="true"/>
          <param name="quant_method" value="area"/>
          <param name="trace_termination_criterion" value="outlier"/>
          <param name="trace_termination_outliers" value="5"/>
          <param name="min_sample_rate" value="0.5"/>
          <param name="min_trace_length" value="5.0"/>
          <param name="max_trace_length" value="-1.0"/>
        </section>
        <section name="epd">
          <param name="enabled" value="true"/>
          <param name="width_filtering" value="fixed"/>
          <param name="min_fwhm" value="3.0"/>
          <param name="max_fwhm" value="60.0"/>
          <param name="masstrace_snr_filtering" value="false"/>
        </section>
        <section name="ffm">
          <param name="local_rt_range" value="10.0"/>
          <param name="local_mz_range" value="6.5"/>
          <param name="charge_lower_bound" value="1"/>
          <param name="charge_upper_bound" value="3"/>
          <param name="report_summed_ints" value="false"/>
          <param name="enable_RT_filtering" value="true"/>
          <param name="isotope_filtering_model" value="none"/>
          <param name="mz_scoring_13C" value="true"/>
          <param name="use_smoothed_intensities" value="true"/>
          <param name="report_convex_hulls" value="true"/>
          <param name="remove_single_traces" value="true"/>
          <param name="mz_scoring_by_elements" value="false"/>
          <param name="elements" value="CHNOPS"/>
        </section>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_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="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
      <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="common">
          <param name="noise_threshold_int" value="10.0"/>
          <param name="chrom_peak_snr" value="3.0"/>
          <param name="chrom_fwhm" value="5.0"/>
        </section>
        <section name="mtd">
          <param name="mass_error_ppm" value="20.0"/>
          <param name="reestimate_mt_sd" value="true"/>
          <param name="quant_method" value="max_height"/>
          <param name="trace_termination_criterion" value="outlier"/>
          <param name="trace_termination_outliers" value="5"/>
          <param name="min_sample_rate" value="0.5"/>
          <param name="min_trace_length" value="5.0"/>
          <param name="max_trace_length" value="300.0"/>
        </section>
        <section name="epd">
          <param name="enabled" value="true"/>
          <param name="width_filtering" value="off"/>
          <param name="min_fwhm" value="3.0"/>
          <param name="max_fwhm" value="60.0"/>
          <param name="masstrace_snr_filtering" value="false"/>
        </section>
        <section name="ffm">
          <param name="local_rt_range" value="10.0"/>
          <param name="local_mz_range" value="6.5"/>
          <param name="charge_lower_bound" value="1"/>
          <param name="charge_upper_bound" value="3"/>
          <param name="report_summed_ints" value="false"/>
          <param name="enable_RT_filtering" value="true"/>
          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
          <param name="mz_scoring_13C" value="true"/>
          <param name="use_smoothed_intensities" value="true"/>
          <param name="report_convex_hulls" value="false"/>
          <param name="remove_single_traces" value="false"/>
          <param name="mz_scoring_by_elements" value="false"/>
          <param name="elements" value="CHNOPS"/>
        </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_FeatureFinderMRM">
    <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="FeatureFinderMRM_1_input.mzML"/>
      <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <param name="min_rt_distance" value="10.0"/>
        <param name="min_num_peaks_per_feature" value="5"/>
        <param name="min_signal_to_noise_ratio" value="2.0"/>
        <param name="write_debug_files" value="false"/>
        <param name="resample_traces" value="false"/>
        <param name="write_debuginfo" 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>
    </test>
  </xml>
  <xml name="autotest_FeatureFinderMultiplex">
    <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="FeatureFinderMultiplex_1_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
        <param name="charge" value="1:4"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="90.0"/>
        <param name="rt_band" value="10.0"/>
        <param name="rt_min" value="5.0"/>
        <param name="mz_tolerance" value="40.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="10.0"/>
        <param name="peptide_similarity" value="0.8"/>
        <param name="averagine_similarity" value="0.75"/>
        <param name="averagine_similarity_scaling" value="0.75"/>
        <param name="missed_cleavages" value="1"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_2_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[][Lys8,Arg10]"/>
        <param name="charge" value="1:4"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="40.0"/>
        <param name="rt_band" value="5.0"/>
        <param name="rt_min" value="2.0"/>
        <param name="mz_tolerance" value="6.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="1000.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.4"/>
        <param name="averagine_similarity_scaling" value="0.75"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_3_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[]"/>
        <param name="charge" value="5:15"/>
        <param name="isotopes_per_peptide" value="5:10"/>
        <param name="rt_typical" value="45.0"/>
        <param name="rt_band" value="5.0"/>
        <param name="rt_min" value="2.0"/>
        <param name="mz_tolerance" value="6.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="200.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.4"/>
        <param name="averagine_similarity_scaling" value="0.75"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="RNA"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_4_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[]"/>
        <param name="charge" value="5:15"/>
        <param name="isotopes_per_peptide" value="5:10"/>
        <param name="rt_typical" value="45.0"/>
        <param name="rt_band" value="5.0"/>
        <param name="rt_min" value="2.0"/>
        <param name="mz_tolerance" value="6.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="200.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.4"/>
        <param name="averagine_similarity_scaling" value="0.75"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="DNA"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_5_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
        <param name="charge" value="1:5"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="50.0"/>
        <param name="rt_band" value="3.0"/>
        <param name="rt_min" value="8.0"/>
        <param name="mz_tolerance" value="10.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="10000000.0"/>
        <param name="peptide_similarity" value="0.95"/>
        <param name="averagine_similarity" value="0.8"/>
        <param name="averagine_similarity_scaling" value="0.95"/>
        <param name="missed_cleavages" value="3"/>
        <param name="spectrum_type" value="profile"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_6_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
        <param name="charge" value="1:5"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="50.0"/>
        <param name="rt_band" value="3.0"/>
        <param name="rt_min" value="8.0"/>
        <param name="mz_tolerance" value="10.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="10000000.0"/>
        <param name="peptide_similarity" value="0.95"/>
        <param name="averagine_similarity" value="0.8"/>
        <param name="averagine_similarity_scaling" value="1.0"/>
        <param name="missed_cleavages" value="3"/>
        <param name="spectrum_type" value="profile"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_7_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[][Dimethyl4]"/>
        <param name="charge" value="1:4"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="40.0"/>
        <param name="rt_band" value="5.0"/>
        <param name="rt_min" value="2.0"/>
        <param name="mz_tolerance" value="6.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="1000.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.4"/>
        <param name="averagine_similarity_scaling" value="0.75"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="31.0094"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_8_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
        <param name="charge" value="1:7"/>
        <param name="isotopes_per_peptide" value="3:8"/>
        <param name="rt_typical" value="50.0"/>
        <param name="rt_band" value="3.0"/>
        <param name="rt_min" value="8.0"/>
        <param name="mz_tolerance" value="10.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="10.0"/>
        <param name="peptide_similarity" value="0.2"/>
        <param name="averagine_similarity" value="0.25"/>
        <param name="averagine_similarity_scaling" value="0.95"/>
        <param name="missed_cleavages" value="4"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="true"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_9_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[0][6.03705]"/>
        <param name="charge" value="2:8"/>
        <param name="isotopes_per_peptide" value="3:8"/>
        <param name="rt_typical" value="40.0"/>
        <param name="rt_band" value="0.0"/>
        <param name="rt_min" value="4.0"/>
        <param name="mz_tolerance" value="10.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="1000.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.4"/>
        <param name="averagine_similarity_scaling" value="0.95"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="centroid"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_10_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
        <param name="charge" value="1:7"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="50.0"/>
        <param name="rt_band" value="5.0"/>
        <param name="rt_min" value="8.0"/>
        <param name="mz_tolerance" value="6.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="10.0"/>
        <param name="peptide_similarity" value="0.4"/>
        <param name="averagine_similarity" value="0.5"/>
        <param name="averagine_similarity_scaling" value="0.95"/>
        <param name="missed_cleavages" value="3"/>
        <param name="spectrum_type" value="profile"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="true"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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="FeatureFinderMultiplex_11_input.mzML"/>
      <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <param name="labels" value="[]"/>
        <param name="charge" value="1:4"/>
        <param name="isotopes_per_peptide" value="3:6"/>
        <param name="rt_typical" value="1e-05"/>
        <param name="rt_band" value="0.0"/>
        <param name="rt_min" value="0.0"/>
        <param name="mz_tolerance" value="10.0"/>
        <param name="mz_unit" value="ppm"/>
        <param name="intensity_cutoff" value="1000.0"/>
        <param name="peptide_similarity" value="0.5"/>
        <param name="averagine_similarity" value="0.7"/>
        <param name="averagine_similarity_scaling" value="0.95"/>
        <param name="missed_cleavages" value="0"/>
        <param name="spectrum_type" value="automatic"/>
        <param name="averagine_type" value="peptide"/>
        <param name="knock_out" value="false"/>
      </section>
      <section name="labels">
        <param name="Arg6" value="6.0201290268"/>
        <param name="Arg10" value="10.0082686"/>
        <param name="Lys4" value="4.0251069836"/>
        <param name="Lys6" value="6.0201290268"/>
        <param name="Lys8" value="8.0141988132"/>
        <param name="Leu3" value="3.01883"/>
        <param name="Dimethyl0" value="28.0313"/>
        <param name="Dimethyl4" value="32.056407"/>
        <param name="Dimethyl6" value="34.063117"/>
        <param name="Dimethyl8" value="36.07567"/>
        <param name="ICPL0" value="105.021464"/>
        <param name="ICPL4" value="109.046571"/>
        <param name="ICPL6" value="111.041593"/>
        <param name="ICPL10" value="115.0667"/>
      </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_FeatureFinderSuperHirn">
    <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="FeatureFinderSuperHirn_input_1.mzML"/>
      <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="centroiding">
          <param name="active" value="false"/>
          <param name="window_width" value="5"/>
          <param name="absolute_isotope_mass_precision" value="0.01"/>
          <param name="relative_isotope_mass_precision" value="10.0"/>
          <param name="minimal_peak_height" value="0.0"/>
          <param name="min_ms_signal_intensity" value="50.0"/>
        </section>
        <section name="ms1">
          <param name="precursor_detection_scan_levels" value="1"/>
          <param name="max_inter_scan_distance" value="0"/>
          <param name="tr_resolution" value="0.01"/>
          <param name="intensity_threshold" value="1000.0"/>
          <param name="max_inter_scan_rt_distance" value="0.1"/>
          <param name="min_nb_cluster_members" value="4"/>
          <param name="detectable_isotope_factor" value="0.05"/>
          <param name="intensity_cv" value="0.9"/>
          <param name="retention_time_tolerance" value="0.5"/>
          <param name="mz_tolerance" value="0.0"/>
        </section>
        <section name="ms1_feature_merger">
          <param name="active" value="true"/>
          <param name="tr_resolution" value="0.01"/>
          <param name="initial_apex_tr_tolerance" value="5.0"/>
          <param name="feature_merging_tr_tolerance" value="1.0"/>
          <param name="intensity_variation_percentage" value="25.0"/>
          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
        </section>
        <section name="ms1_feature_selection_options">
          <param name="start_elution_window" value="0.0"/>
          <param name="end_elution_window" value="180.0"/>
          <param name="mz_range_min" value="0.0"/>
          <param name="mz_range_max" value="2000.0"/>
          <param name="chrg_range_min" value="1"/>
          <param name="chrg_range_max" value="5"/>
        </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="FeatureFinderSuperHirn_input_2.mzML"/>
      <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <section name="algorithm">
        <section name="centroiding">
          <param name="active" value="true"/>
          <param name="window_width" value="5"/>
          <param name="absolute_isotope_mass_precision" value="0.01"/>
          <param name="relative_isotope_mass_precision" value="10.0"/>
          <param name="minimal_peak_height" value="0.0"/>
          <param name="min_ms_signal_intensity" value="50.0"/>
        </section>
        <section name="ms1">
          <param name="precursor_detection_scan_levels" value="1"/>
          <param name="max_inter_scan_distance" value="0"/>
          <param name="tr_resolution" value="0.01"/>
          <param name="intensity_threshold" value="1000.0"/>
          <param name="max_inter_scan_rt_distance" value="0.1"/>
          <param name="min_nb_cluster_members" value="4"/>
          <param name="detectable_isotope_factor" value="0.05"/>
          <param name="intensity_cv" value="0.9"/>
          <param name="retention_time_tolerance" value="0.5"/>
          <param name="mz_tolerance" value="0.0"/>
        </section>
        <section name="ms1_feature_merger">
          <param name="active" value="true"/>
          <param name="tr_resolution" value="0.01"/>
          <param name="initial_apex_tr_tolerance" value="5.0"/>
          <param name="feature_merging_tr_tolerance" value="1.0"/>
          <param name="intensity_variation_percentage" value="25.0"/>
          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
        </section>
        <section name="ms1_feature_selection_options">
          <param name="start_elution_window" value="0.0"/>
          <param name="end_elution_window" value="180.0"/>
          <param name="mz_range_min" value="0.0"/>
          <param name="mz_range_max" value="2000.0"/>
          <param name="chrg_range_min" value="1"/>
          <param name="chrg_range_max" value="5"/>
        </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_FeatureLinkerLabeled">
    <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="FeatureLinkerLabeled_1_input.featureXML"/>
      <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="rt_estimate" value="false"/>
        <param name="rt_pair_dist" value="-1.0"/>
        <param name="rt_dev_low" value="0.4"/>
        <param name="rt_dev_high" value="0.4"/>
        <param name="mz_pair_dists" value="8.0"/>
        <param name="mz_dev" value="0.1"/>
        <param name="mrm" 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>
    </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="FeatureLinkerLabeled_2_input.featureXML"/>
      <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="rt_estimate" value="true"/>
        <param name="rt_pair_dist" value="-121.0382"/>
        <param name="rt_dev_low" value="123.3965"/>
        <param name="rt_dev_high" value="123.3965"/>
        <param name="mz_pair_dists" value="4.0"/>
        <param name="mz_dev" value="0.1"/>
        <param name="mrm" 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>
    </test>
  </xml>
  <xml name="autotest_FeatureLinkerUnlabeledKD">
    <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="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="Da"/>
        <param name="nr_partitions" value="1"/>
        <section name="warp">
          <param name="enabled" value="false"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="charge_merging" value="With_charge_zero"/>
          <param name="adduct_merging" value="Any"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="true"/>
      <section name="algorithm">
        <param name="mz_unit" value="Da"/>
        <param name="nr_partitions" value="99999"/>
        <section name="warp">
          <param name="enabled" value="false"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="charge_merging" value="With_charge_zero"/>
          <param name="adduct_merging" value="Any"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="Da"/>
        <param name="nr_partitions" value="100"/>
        <section name="warp">
          <param name="enabled" value="false"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="0.3"/>
          <param name="charge_merging" value="With_charge_zero"/>
          <param name="adduct_merging" value="Any"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="ppm"/>
        <param name="nr_partitions" value="100"/>
        <section name="warp">
          <param name="enabled" value="true"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="5.0"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="30.0"/>
          <param name="mz_tol" value="10.0"/>
          <param name="charge_merging" value="Identical"/>
          <param name="adduct_merging" value="Any"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="ppm"/>
        <param name="nr_partitions" value="100"/>
        <section name="warp">
          <param name="enabled" value="true"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="5.0"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="30.0"/>
          <param name="mz_tol" value="10.0"/>
          <param name="charge_merging" value="With_charge_zero"/>
          <param name="adduct_merging" value="Any"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="ppm"/>
        <param name="nr_partitions" value="100"/>
        <section name="warp">
          <param name="enabled" value="true"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="5.0"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="30.0"/>
          <param name="mz_tol" value="10.0"/>
          <param name="charge_merging" value="Any"/>
          <param name="adduct_merging" value="With_unknown_adducts"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="mz_unit" value="ppm"/>
        <param name="nr_partitions" value="100"/>
        <section name="warp">
          <param name="enabled" value="true"/>
          <param name="rt_tol" value="100.0"/>
          <param name="mz_tol" value="5.0"/>
          <param name="max_pairwise_log_fc" value="0.5"/>
          <param name="min_rel_cc_size" value="0.5"/>
          <param name="max_nr_conflicts" value="0"/>
        </section>
        <section name="link">
          <param name="rt_tol" value="30.0"/>
          <param name="mz_tol" value="10.0"/>
          <param name="charge_merging" value="Any"/>
          <param name="adduct_merging" value="Identical"/>
        </section>
        <section name="distance_RT">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
          <param name="log_transform" value="enabled"/>
        </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>
      <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_FeatureLinkerUnlabeledQT">
    <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="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="use_identifications" value="false"/>
        <param name="nr_partitions" value="100"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="100.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="true"/>
      <section name="algorithm">
        <param name="use_identifications" value="false"/>
        <param name="nr_partitions" value="100"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="100.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="use_identifications" value="false"/>
        <param name="nr_partitions" value="99999"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="100.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="use_identifications" value="true"/>
        <param name="nr_partitions" value="100"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="100.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="use_identifications" value="false"/>
        <param name="nr_partitions" value="100"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="200.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="use_identifications" value="true"/>
        <param name="nr_partitions" value="100"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="200.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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_FeatureLinkerUnlabeled">
    <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="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="second_nearest_gap" value="2.0"/>
        <param name="use_identifications" value="false"/>
        <param name="ignore_charge" value="true"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="200.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.5"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="second_nearest_gap" value="2.0"/>
        <param name="use_identifications" value="false"/>
        <param name="ignore_charge" value="false"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="100.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.5"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="second_nearest_gap" value="1.5"/>
        <param name="use_identifications" value="false"/>
        <param name="ignore_charge" value="true"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="30.0"/>
          <param name="exponent" value="1.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.3"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
      <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="keep_subelements" value="false"/>
      <section name="algorithm">
        <param name="second_nearest_gap" value="2.0"/>
        <param name="use_identifications" value="true"/>
        <param name="ignore_charge" value="true"/>
        <param name="ignore_adduct" value="true"/>
        <section name="distance_RT">
          <param name="max_difference" value="200.0"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_MZ">
          <param name="max_difference" value="0.5"/>
          <param name="unit" value="Da"/>
          <param name="exponent" value="2.0"/>
          <param name="weight" value="1.0"/>
        </section>
        <section name="distance_intensity">
          <param name="exponent" value="1.0"/>
          <param name="weight" value="0.0"/>
          <param name="log_transform" value="disabled"/>
        </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_FFEval">
</xml>
  <xml name="autotest_FidoAdapter">
    <test expect_num_outputs="2">
      <conditional name="adv_opts_cond">
        <param name="adv_opts_selector" value="advanced"/>
        <param name="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <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="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.0"/>
        <param name="peptide" value="0.0"/>
        <param name="spurious" value="0.0"/>
      </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="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <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_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="separate_runs" value="true"/>
      <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="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.0"/>
        <param name="peptide" value="0.0"/>
        <param name="spurious" value="0.0"/>
      </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="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <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_3_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="true"/>
      <param name="group_level" value="true"/>
      <param name="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.0"/>
        <param name="peptide" value="0.0"/>
        <param name="spurious" value="0.0"/>
      </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="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <param name="log2_states_precalc" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_4_input.idXML"/>
      <output name="out" file="FidoAdapter_4_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="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.0"/>
        <param name="peptide" value="0.0"/>
        <param name="spurious" value="0.0"/>
      </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="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <param name="log2_states_precalc" value="0"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FidoAdapter_5_input.idXML"/>
      <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
      <param name="separate_runs" value="false"/>
      <param name="greedy_group_resolution" value="true"/>
      <param name="no_cleanup" value="false"/>
      <param name="all_PSMs" value="false"/>
      <param name="group_level" value="false"/>
      <param name="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.0"/>
        <param name="peptide" value="0.0"/>
        <param name="spurious" value="0.0"/>
      </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="keep_zero_group" value="false"/>
        <param name="accuracy" value=""/>
        <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="log2_states" value="0"/>
      <section name="prob">
        <param name="protein" value="0.9"/>
        <param name="peptide" value="0.01"/>
        <param name="spurious" value="0.0"/>
      </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_FileConverter">
    <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_1_input.mzData"/>
      <output name="out" file="FileConverter_1_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_2_input.someInputDTA2D"/>
      <output name="out" file="FileConverter_2_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_3_input.featureXML"/>
      <output name="out" file="FileConverter_3_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_4_input.mzXML"/>
      <output name="out" file="FileConverter_4_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_5_input.mzML"/>
      <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <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_6_input.mzML"/>
      <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <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_7_input.consensusXML"/>
      <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_8_input.mzML"/>
      <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
      <param name="out_type" value="mzData"/>
      <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_9_input.consensusXML"/>
      <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_10_input.edta" ftype="edta"/>
      <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_11_input.peplist"/>
      <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_12_input.peptides.tsv" ftype="tabular"/>
      <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_13_input.peptides.kroenik"/>
      <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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_9_output.featureXML"/>
      <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <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_10_input.edta" ftype="edta"/>
      <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <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_16_input.edta" ftype="edta"/>
      <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <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_17_input.consensusXML"/>
      <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="out_type" value="csv"/>
      <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_17_input.consensusXML"/>
      <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
      <param name="out_type" value="csv"/>
      <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="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" file="FileConverter_19_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_20_input.featureXML"/>
      <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <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="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileConverter_4_input.mzXML"/>
      <output name="out" file="FileConverter_4_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_23_input.mzML"/>
      <output name="out" file="FileConverter_23_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="true"/>
        <param name="lossy_mass_accuracy" value="0.0001"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" file="FileConverter_24_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="true"/>
        <param name="lossy_mass_accuracy" value="-1.0"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="FileFilter_1_input.mzML"/>
      <output name="out" file="FileConverter_25_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="true"/>
        <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <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="true"/>
        <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_26_output.mzXML"/>
      <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
      <param name="out_type" value="mzXML"/>
      <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="true"/>
        <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_27_input.mzML"/>
      <output name="out" file="FileConverter_27_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="true"/>
        <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_28_input.mzML"/>
      <output name="out" file="FileConverter_28_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="true"/>
        <param name="lossy_mass_accuracy" value="1e-05"/>
        <param name="process_lowmemory" value="true"/>
        <param name="no_peak_picking" value="false"/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </conditional>
      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
      <output name="out" file="FileConverter_29_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_29_output.mzML"/>
      <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/>
      <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="multiple"/>
        <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_30_input.mzML"/>
      <output name="out" file="FileConverter_30_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="single"/>
        <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_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="ginkgotoxin-ms-switching.raw"/>
      <output name="out" file="ginkgotoxin-ms-switching_out_tmp.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>
  </xml>
  <xml name="autotest_FileFilter">
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":30"/>
      <param name="mz" value=":1000"/>
      <param name="int" value=":20000"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value="30:"/>
      <param name="mz" value="1000:"/>
      <param name="int" value="100:"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="2"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_4_input.mzML"/>
      <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="true"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_5_input.featureXML"/>
      <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="rt" value=":1000"/>
      <param name="mz" value=":480"/>
      <param name="int" value=":79000"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":0.6"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":3"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_5_input.featureXML"/>
      <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="rt" value="1000:"/>
      <param name="mz" value="440:"/>
      <param name="int" value="70000:"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value="0.51:"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value="3:"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_7_input.mzML"/>
      <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value="7000:"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_8_input.consensusXML"/>
      <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="rt" value="600:1400"/>
      <param name="mz" value="700:2300"/>
      <param name="int" value="1100:6000"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_9_input.mzML"/>
      <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value="SelectedIonMonitoring"/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_10_input.mzML"/>
      <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value="Collision-induced dissociation"/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_11_input.mzML"/>
      <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value="Plasma desorption"/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_12_input.mzML"/>
      <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="true"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_13_input.consensusXML"/>
      <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featureXML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value="2"/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_14_input.consensusXML"/>
      <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusXML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value="0 2"/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_15_input.featureXML"/>
      <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featurexml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="true"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_15_input.featureXML"/>
      <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featurexml"/>
      <param name="rt" value="3000:4000"/>
      <param name="mz" value="400:600"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="true"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_15_input.featureXML"/>
      <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featurexml"/>
      <param name="rt" value="3000:4000"/>
      <param name="mz" value="400:600"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="true"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_18_input.consensusXML"/>
      <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusxml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="true"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_18_input.consensusXML"/>
      <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusxml"/>
      <param name="rt" value="3000:4000"/>
      <param name="mz" value="400:600"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="true"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_15_input.featureXML"/>
      <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featurexml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="true"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_15_input.featureXML"/>
      <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
      <param name="out_type" value="featurexml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="true"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="true"/>
        <param name="remove_unassigned_ids" value="true"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_22_input.consensusXML"/>
      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusxml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_22_input.consensusXML"/>
      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusxml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_22_input.consensusXML"/>
      <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
      <param name="out_type" value="consensusxml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_25_input.mzML.gz"/>
      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="blacklist" value="FileFilter_25_input.idXML"/>
        <param name="rt" value="1.0"/>
        <param name="mz" value="0.05"/>
        <param name="blacklist_imperfect" value="true"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_25_input.mzML.gz"/>
      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="blacklist" value="FileFilter_25_input.idXML"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="true"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_28_input.mzML.gz"/>
      <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value="832:836"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="2"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_28_input.mzML.gz"/>
      <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value="832:836"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_28_input.mzML.gz"/>
      <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value="832:836"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_31_34_input.mzML"/>
      <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":2"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_31_34_input.mzML"/>
      <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":2"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_31_34_input.mzML"/>
      <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":35"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_31_34_input.mzML"/>
      <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzml"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":35"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="false"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="linear"/>
          <param name="lossy_mass_accuracy" value="0.0001"/>
          <param name="intensity" value="slof"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_1_input.mzML"/>
      <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="linear"/>
          <param name="lossy_mass_accuracy" value="0.0001"/>
          <param name="intensity" value="pic"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_40_input.mzML"/>
      <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value="positive"/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_40_input.mzML"/>
      <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value="negative"/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_40_input.mzML"/>
      <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <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>
    <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="FileFilter_43_input.mzML"/>
      <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
      <param name="out_type" value="mzML"/>
      <param name="rt" value=":"/>
      <param name="mz" value=":"/>
      <param name="int" value=":"/>
      <param name="sort" value="false"/>
      <section name="peak_options">
        <param name="sn" value="0.0"/>
        <param name="rm_pc_charge" value=""/>
        <param name="pc_mz_range" value=":"/>
        <param name="pc_mz_list" value=""/>
        <param name="level" value="1 2 3"/>
        <param name="sort_peaks" value="false"/>
        <param name="no_chromatograms" value="false"/>
        <param name="remove_chromatograms" value="false"/>
        <param name="remove_empty" value="false"/>
        <param name="mz_precision" value="64"/>
        <param name="int_precision" value="32"/>
        <param name="indexed_file" value="true"/>
        <param name="zlib_compression" value="false"/>
        <section name="numpress">
          <param name="masstime" value="none"/>
          <param name="lossy_mass_accuracy" value="-1.0"/>
          <param name="intensity" value="none"/>
          <param name="float_da" value="none"/>
        </section>
      </section>
      <section name="spectra">
        <param name="remove_zoom" value="false"/>
        <param name="remove_mode" value=""/>
        <param name="remove_activation" value=""/>
        <param name="remove_collision_energy" value=":"/>
        <param name="remove_isolation_window_width" value=":"/>
        <param name="select_zoom" value="false"/>
        <param name="select_mode" value=""/>
        <param name="select_activation" value=""/>
        <param name="select_collision_energy" value=":"/>
        <param name="select_isolation_window_width" value=":"/>
        <param name="select_polarity" value=""/>
        <section name="blackorwhitelist">
          <param name="similarity_threshold" value="-1.0"/>
          <param name="rt" value="0.01"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
          <param name="blacklist" value="true"/>
        </section>
      </section>
      <section name="feature">
        <param name="q" value=":"/>
      </section>
      <section name="consensus">
        <param name="map" value=""/>
        <param name="map_and" value="false"/>
        <section name="blackorwhitelist">
          <param name="blacklist" value="true"/>
          <param name="maps" value=""/>
          <param name="rt" value="60.0"/>
          <param name="mz" value="0.01"/>
          <param name="use_ppm_tolerance" value="false"/>
        </section>
      </section>
      <section name="f_and_c">
        <param name="charge" value=":"/>
        <param name="size" value=":"/>
        <param name="remove_meta" value=""/>
      </section>
      <section name="id">
        <param name="remove_clashes" value="false"/>
        <param name="keep_best_score_id" value="false"/>
        <param name="sequences_whitelist" value=""/>
        <param name="sequence_comparison_method" value="substring"/>
        <param name="accessions_whitelist" value=""/>
        <param name="remove_annotated_features" value="false"/>
        <param name="remove_unannotated_features" value="false"/>
        <param name="remove_unassigned_ids" value="false"/>
        <param name="rt" value="0.1"/>
        <param name="mz" value="0.001"/>
        <param name="blacklist_imperfect" value="false"/>
      </section>
      <section name="algorithm">
        <section name="SignalToNoise">
          <param name="max_intensity" value="-1"/>
          <param name="auto_max_stdev_factor"