diff macros_autotest.xml @ 10:7a9d97cfe93c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:40:20 +0000
parents 4c485bb20e27
children
line wrap: on
line diff
--- a/macros_autotest.xml	Thu Sep 24 12:10:26 2020 +0000
+++ b/macros_autotest.xml	Tue Oct 13 20:40:20 2020 +0000
@@ -158,7 +158,6 @@
         <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"/>
@@ -228,7 +227,6 @@
         <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"/>
@@ -298,7 +296,6 @@
         <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"/>
@@ -368,7 +365,6 @@
         <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"/>
@@ -438,7 +434,6 @@
         <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"/>
@@ -508,7 +503,6 @@
         <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"/>
@@ -578,7 +572,6 @@
         <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"/>
@@ -648,7 +641,6 @@
         <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"/>
@@ -718,7 +710,6 @@
         <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"/>
@@ -760,9 +751,6 @@
     <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"/>
@@ -770,6 +758,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -781,7 +770,7 @@
         <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="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="spectra_comet.mzML"/>
@@ -791,9 +780,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -803,6 +798,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -813,9 +809,6 @@
     <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"/>
@@ -823,6 +816,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="1000"/>
@@ -834,7 +828,7 @@
         <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="force" value="true"/>
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="CometAdapter_2_prepared.mzML"/>
@@ -844,9 +838,15 @@
       <param name="precursor_mass_tolerance" value="3.0"/>
       <param name="precursor_error_units" value="Da"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.50025"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.25"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="1"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep any known"/>
@@ -856,6 +856,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value=""/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -866,9 +867,6 @@
     <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"/>
@@ -876,6 +874,7 @@
         <param name="use_Y_ions" value="true"/>
         <param name="use_Z_ions" value="false"/>
         <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
         <param name="digest_mass_range" value="600:5000"/>
         <param name="max_precursor_charge" value="5"/>
         <param name="spectrum_batch_size" value="20000"/>
@@ -897,9 +896,15 @@
       <param name="precursor_mass_tolerance" value="5.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
       <param name="enzyme" value="Trypsin"/>
       <param name="num_enzyme_termini" value="fully"/>
-      <param name="allowed_missed_cleavages" value="3"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
       <param name="num_hits" value="5"/>
       <param name="precursor_charge" value="0:0"/>
       <param name="override_charge" value="keep known search unknown"/>
@@ -909,6 +914,7 @@
       <param name="clip_nterm_methionine" value="false"/>
       <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
       <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
+      <param name="binary_modifications" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -916,6 +922,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="use_A_ions" value="false"/>
+        <param name="use_B_ions" value="true"/>
+        <param name="use_C_ions" value="false"/>
+        <param name="use_X_ions" value="false"/>
+        <param name="use_Y_ions" value="true"/>
+        <param name="use_Z_ions" value="false"/>
+        <param name="use_NL_ions" value="false"/>
+        <param name="second_enzyme" value=""/>
+        <param name="digest_mass_range" value="600:1200"/>
+        <param name="max_precursor_charge" value="5"/>
+        <param name="spectrum_batch_size" value="20000"/>
+        <param name="mass_offsets" value="0.0"/>
+        <param name="minimum_peaks" value="10"/>
+        <param name="minimum_intensity" value="0.0"/>
+        <param name="remove_precursor_peak" value="no"/>
+        <param name="remove_precursor_tolerance" value="1.5"/>
+        <param name="clear_mz_range" value="0:0"/>
+        <param name="max_variable_mods_in_peptide" value="3"/>
+        <param name="require_variable_mod" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
+      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="isotope_error" value="off"/>
+      <param name="fragment_mass_tolerance" value="0.01"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="fragment_bin_offset" value="0.0"/>
+      <param name="instrument" value="high_res"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="num_enzyme_termini" value="fully"/>
+      <param name="missed_cleavages" value="3"/>
+      <param name="min_peptide_length" value="5"/>
+      <param name="max_peptide_length" value="63"/>
+      <param name="num_hits" value="5"/>
+      <param name="precursor_charge" value="0:0"/>
+      <param name="override_charge" value="keep known search unknown"/>
+      <param name="ms_level" value="2"/>
+      <param name="activation_method" value="ALL"/>
+      <param name="max_fragment_charge" value="3"/>
+      <param name="clip_nterm_methionine" value="false"/>
+      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
+      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
+      <param name="binary_modifications" value=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_CompNovoCID">
     <test expect_num_outputs="2">
@@ -1006,11 +1069,13 @@
       <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1037,11 +1102,13 @@
       <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="average"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1068,11 +1135,13 @@
       <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1099,11 +1168,13 @@
       <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPMatrix"/>
       <section name="filter">
         <param name="considered_hits" value="6"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1130,11 +1201,13 @@
       <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="PEPIons"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.0"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1161,11 +1234,79 @@
       <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="rt_delta" value="0.1"/>
       <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="false"/>
       <param name="algorithm" value="best"/>
       <section name="filter">
         <param name="considered_hits" value="0"/>
         <param name="min_support" value="0.5"/>
         <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="false"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_6_input.idXML"/>
+      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
+      </section>
+      <section name="PEPIons">
+        <param name="mass_tolerance" value="0.5"/>
+        <param name="min_shared" value="2"/>
+      </section>
+      <section name="PEPMatrix">
+        <param name="matrix" value="identity"/>
+        <param name="penalty" value="5"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="ConsensusID_8_input.idXML"/>
+      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="rt_delta" value="0.1"/>
+      <param name="mz_delta" value="0.1"/>
+      <param name="per_spectrum" value="true"/>
+      <param name="algorithm" value="best"/>
+      <section name="filter">
+        <param name="considered_hits" value="0"/>
+        <param name="min_support" value="0.0"/>
+        <param name="count_empty" value="false"/>
+        <param name="keep_old_scores" value="true"/>
       </section>
       <section name="PEPIons">
         <param name="mass_tolerance" value="0.5"/>
@@ -1230,7 +1371,7 @@
       <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="decoy_format" value="peptide-reverse"/>
       <param name="keep_terminal_aminos" value="NC"/>
       <param name="cterm_modifications" value=""/>
       <param name="nterm_modifications" value=""/>
@@ -1317,6 +1458,74 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_DatabaseSuitability">
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.8"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.9"/>
+        <param name="FDR" value="1.0"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="true"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.9"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_Decharger">
     <test expect_num_outputs="4">
       <conditional name="adv_opts_cond">
@@ -1475,6 +1684,8 @@
   </xml>
   <xml name="autotest_DeMeanderize">
 </xml>
+  <xml name="autotest_DigestorMotif">
+</xml>
   <xml name="autotest_Digestor">
 </xml>
   <xml name="autotest_DTAExtractor">
@@ -1546,12 +1757,14 @@
       </conditional>
       <param name="in" value="FidoAdapter_1_input.idXML"/>
       <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idxml"/>
       <param name="protein_fdr" value="false"/>
       <param name="greedy_group_resolution" value="none"/>
       <param name="max_psms_extreme_probability" value="1.0"/>
       <section name="algorithm">
         <param name="psm_probability_cutoff" value="0.001"/>
         <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
         <param name="update_PSM_probabilities" value="true"/>
         <param name="user_defined_priors" value="false"/>
         <param name="annotate_group_probabilities" value="true"/>
@@ -1574,6 +1787,107 @@
         <section name="param_optimize">
           <param name="aucweight" value="0.3"/>
           <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="true"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="conservative_fdr" value="true"/>
+        <param name="min_psms_extreme_probability" value="0.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_input.consensusXML"/>
+      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="out_type" value="consensusXML"/>
+      <param name="protein_fdr" value="false"/>
+      <param name="greedy_group_resolution" value="none"/>
+      <param name="max_psms_extreme_probability" value="1.0"/>
+      <section name="algorithm">
+        <param name="psm_probability_cutoff" value="0.001"/>
+        <param name="top_PSMs" value="1"/>
+        <param name="keep_best_PSM_only" value="false"/>
+        <param name="update_PSM_probabilities" value="true"/>
+        <param name="user_defined_priors" value="false"/>
+        <param name="annotate_group_probabilities" value="true"/>
+        <param name="use_ids_outside_features" value="false"/>
+        <section name="model_parameters">
+          <param name="prot_prior" value="0.7"/>
+          <param name="pep_emission" value="0.1"/>
+          <param name="pep_spurious_emission" value="0.001"/>
+          <param name="pep_prior" value="0.1"/>
+          <param name="regularize" value="false"/>
+          <param name="extended_model" value="false"/>
+        </section>
+        <section name="loopy_belief_propagation">
+          <param name="scheduling_type" value="priority"/>
+          <param name="convergence_threshold" value="1e-05"/>
+          <param name="dampening_lambda" value="0.001"/>
+          <param name="max_nr_iterations" value="2147483647"/>
+          <param name="p_norm_inference" value="1.0"/>
+        </section>
+        <section name="param_optimize">
+          <param name="aucweight" value="0.3"/>
+          <param name="conservative_fdr" value="true"/>
+          <param name="regularized_fdr" value="true"/>
         </section>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -1976,6 +2290,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2031,61 +2346,7 @@
         <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"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -2129,6 +2390,7 @@
         <param name="add_zeros" value="0.2"/>
         <param name="unweighted_fit" value="false"/>
         <param name="no_imputation" value="false"/>
+        <param name="each_trace" value="false"/>
         <section name="check">
           <param name="min_area" value="1.0"/>
           <param name="boundaries" value="0.5"/>
@@ -4074,7 +4336,7 @@
         <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"/>
+      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <param name="separate_runs" value="false"/>
       <param name="greedy_group_resolution" value="false"/>
       <param name="no_cleanup" value="false"/>
@@ -5009,6 +5271,34 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
+      <param name="in" value="FileConverter_32_input.mzML"/>
+      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
+      <param name="out_type" value="mzML"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </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"/>
@@ -11129,6 +11419,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11154,6 +11446,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11179,6 +11473,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11203,6 +11499,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11228,6 +11526,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11253,6 +11553,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11277,6 +11579,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11301,6 +11605,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11325,6 +11631,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11349,6 +11657,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11373,6 +11683,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11397,6 +11709,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11421,6 +11735,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11445,6 +11761,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11470,6 +11788,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11494,6 +11814,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11518,6 +11840,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11542,6 +11866,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11566,6 +11892,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11590,6 +11918,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11615,6 +11945,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.01"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11640,6 +11972,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11664,6 +11998,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11688,6 +12024,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11712,6 +12050,8 @@
         <param name="no_spectra_data_override" value="false"/>
         <param name="no_spectra_references_override" value="false"/>
         <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
@@ -11728,6 +12068,136 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="-1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="true"/>
+        <param name="number_of_hits" value="2"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_27_input.idXML"/>
+      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
+      <param name="out_type" value="FASTA"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="ignore_proteins_per_peptide" value="false"/>
+        <param name="scan_regex" value=""/>
+        <param name="no_spectra_data_override" value="false"/>
+        <param name="no_spectra_references_override" value="false"/>
+        <param name="add_ionmatch_annotation" value="0.0"/>
+        <param name="concatenate_peptides" value="false"/>
+        <param name="number_of_hits" value="1"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDFileConverter_31_input.mzid"/>
+      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="out_type" value="idXML"/>
+      <param name="mz_name" value=""/>
+      <param name="peptideprophet_analyzed" value="false"/>
+      <param name="score_type" value="qvalue"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_IDFilter">
     <test expect_num_outputs="2">
@@ -11754,6 +12224,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="proteins" value="IDFilter_1_input.fas"/>
@@ -11821,6 +12292,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11888,6 +12360,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -11954,6 +12427,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12020,6 +12494,7 @@
       <section name="score">
         <param name="pep" value="32.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12086,6 +12561,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12152,6 +12628,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="25.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12218,6 +12695,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12284,6 +12762,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12350,6 +12829,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12416,6 +12896,7 @@
       <section name="score">
         <param name="pep" value="0.05"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12482,6 +12963,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.3"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12548,6 +13030,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12614,6 +13097,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12681,6 +13165,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12748,6 +13233,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12815,6 +13301,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12882,6 +13369,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -12949,6 +13437,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13015,6 +13504,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13081,6 +13571,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13147,6 +13638,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13213,6 +13705,7 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13279,6 +13772,141 @@
       <section name="score">
         <param name="pep" value="0.0"/>
         <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDMapper_2_output.consensusXML"/>
+      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.0"/>
+      </section>
+      <section name="whitelist">
+        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="blacklist">
+        <param name="protein_accessions" value=""/>
+        <param name="ignore_modifications" value="false"/>
+        <param name="modifications" value=""/>
+      </section>
+      <section name="in_silico_digestion">
+        <param name="enzyme" value="Trypsin"/>
+        <param name="specificity" value="full"/>
+        <param name="missed_cleavages" value="-1"/>
+        <param name="methionine_cleavage" value="false"/>
+      </section>
+      <section name="missed_cleavages">
+        <param name="number_of_missed_cleavages" value=":"/>
+        <param name="enzyme" value="Trypsin"/>
+      </section>
+      <section name="rt">
+        <param name="p_value" value="0.0"/>
+        <param name="p_value_1st_dim" value="0.0"/>
+      </section>
+      <section name="mz">
+        <param name="error" value="-1.0"/>
+        <param name="unit" value="ppm"/>
+      </section>
+      <section name="best">
+        <param name="n_peptide_hits" value="0"/>
+        <param name="n_protein_hits" value="0"/>
+        <param name="strict" value="false"/>
+        <param name="n_to_m_peptide_hits" value=":"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="remove_duplicate_psm" value="false"/>
+        <param name="remove_peptide_hits_by_metavalue" value=""/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_3_out.consensusXML"/>
+      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <param name="var_mods" value="false"/>
+      <param name="remove_shared_peptides" value="false"/>
+      <param name="keep_unreferenced_protein_hits" value="false"/>
+      <param name="remove_decoys" value="false"/>
+      <param name="delete_unreferenced_peptide_hits" value="false"/>
+      <section name="precursor">
+        <param name="rt" value=":"/>
+        <param name="mz" value=":"/>
+        <param name="length" value=":"/>
+        <param name="charge" value=":"/>
+      </section>
+      <section name="score">
+        <param name="pep" value="0.0"/>
+        <param name="prot" value="0.0"/>
+        <param name="protgroup" value="0.99"/>
       </section>
       <section name="whitelist">
         <param name="protein_accessions" value=""/>
@@ -13882,11 +14510,11 @@
       </conditional>
       <param name="in" value="IDFileConverter_12_output.idXML"/>
       <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="false"/>
       <param name="new_score" value="Percolator_PEP"/>
       <param name="new_score_orientation" value="lower_better"/>
       <param name="new_score_type" value="Posterior Error Probability"/>
       <param name="old_score" value="Percolator_qvalue"/>
-      <param name="proteins" value="false"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -13902,11 +14530,11 @@
       </conditional>
       <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
       <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="proteins" value="true"/>
       <param name="new_score" value="Posterior Probability_score"/>
       <param name="new_score_orientation" value="higher_better"/>
       <param name="new_score_type" value="Posterior Probability"/>
       <param name="old_score" value=""/>
-      <param name="proteins" value="true"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
@@ -14453,80 +15081,6 @@
   </xml>
   <xml name="autotest_LabeledEval">
 </xml>
-  <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_LowMemPeakPickerHiRes">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
   <xml name="autotest_LuciphorAdapter">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -14894,6 +15448,63 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="true"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
+      <output_collection name="out" count="1"/>
+      <output_collection name="trafo_out" count="1"/>
+      <section name="reference">
+        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
+        <param name="index" value="0"/>
+      </section>
+      <section name="algorithm">
+        <param name="score_cutoff" value="false"/>
+        <param name="min_score" value="0.05"/>
+        <param name="min_run_occur" value="2"/>
+        <param name="max_rt_shift" value="0.5"/>
+        <param name="use_unassigned_peptides" value="true"/>
+        <param name="use_feature_rt" value="false"/>
+      </section>
+      <section name="model">
+        <param name="type" value="b_spline"/>
+        <section name="linear">
+          <param name="symmetric_regression" value="false"/>
+          <param name="x_weight" value=""/>
+          <param name="y_weight" value=""/>
+          <param name="x_datum_min" value="1e-15"/>
+          <param name="x_datum_max" value="1000000000000000.0"/>
+          <param name="y_datum_min" value="1e-15"/>
+          <param name="y_datum_max" value="1000000000000000.0"/>
+        </section>
+        <section name="b_spline">
+          <param name="wavelength" value="0.0"/>
+          <param name="num_nodes" value="5"/>
+          <param name="extrapolate" value="linear"/>
+          <param name="boundary_condition" value="2"/>
+        </section>
+        <section name="lowess">
+          <param name="span" value="0.666666666666667"/>
+          <param name="num_iterations" value="3"/>
+          <param name="delta" value="-1.0"/>
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="four-point-linear"/>
+        </section>
+        <section name="interpolated">
+          <param name="interpolation_type" value="cspline"/>
+          <param name="extrapolation_type" value="two-point-linear"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapAlignerPoseClustering">
     <test expect_num_outputs="3">
@@ -15281,6 +15892,61 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
+      <output_collection name="out" count="3"/>
+      <section name="algorithm">
+        <param name="model_type" value="b_spline"/>
+        <section name="model">
+          <param name="type" value="b_spline"/>
+          <section name="linear">
+            <param name="symmetric_regression" value="false"/>
+            <param name="x_weight" value=""/>
+            <param name="y_weight" value=""/>
+            <param name="x_datum_min" value="1e-15"/>
+            <param name="x_datum_max" value="1000000000000000.0"/>
+            <param name="y_datum_min" value="1e-15"/>
+            <param name="y_datum_max" value="1000000000000000.0"/>
+          </section>
+          <section name="b_spline">
+            <param name="wavelength" value="0.0"/>
+            <param name="num_nodes" value="5"/>
+            <param name="extrapolate" value="linear"/>
+            <param name="boundary_condition" value="2"/>
+          </section>
+          <section name="lowess">
+            <param name="span" value="0.666666666666667"/>
+            <param name="num_iterations" value="3"/>
+            <param name="delta" value="-1.0"/>
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="four-point-linear"/>
+          </section>
+          <section name="interpolated">
+            <param name="interpolation_type" value="cspline"/>
+            <param name="extrapolation_type" value="two-point-linear"/>
+          </section>
+        </section>
+        <section name="align_algorithm">
+          <param name="score_cutoff" value="false"/>
+          <param name="min_score" value="0.05"/>
+          <param name="min_run_occur" value="2"/>
+          <param name="max_rt_shift" value="0.5"/>
+          <param name="use_unassigned_peptides" value="true"/>
+          <param name="use_feature_rt" value="true"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_MapNormalizer">
     <test expect_num_outputs="2">
@@ -15651,9 +16317,8 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="true"/>
-      <param name="mascot_out" value="false"/>
+      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
+      <param name="out_type" value="mgf"/>
       <param name="instrument" value="ESI-TRAP"/>
       <param name="precursor_mass_tolerance" value="1.3"/>
       <param name="peak_mass_tolerance" value="0.3"/>
@@ -15691,8 +16356,7 @@
       </conditional>
       <param name="in" value="MascotAdapter_2_input.mascotXML"/>
       <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="mascot_in" value="false"/>
-      <param name="mascot_out" value="true"/>
+      <param name="out_type" value="idXML"/>
       <param name="instrument" value="Default"/>
       <param name="precursor_mass_tolerance" value="2.0"/>
       <param name="peak_mass_tolerance" value="1.0"/>
@@ -15730,9 +16394,9 @@
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </conditional>
-      <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/>
+      <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
       <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="0 1"/>
       <param name="format" value="table"/>
       <param name="average_mass" value="false"/>
@@ -15752,7 +16416,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
+      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
       <param name="charge" value="1 2 3"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -15849,7 +16513,80 @@
     </test>
   </xml>
   <xml name="autotest_MetaboliteAdductDecharger">
-</xml>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
+      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
+      <section name="algorithm">
+        <section name="MetaboliteFeatureDeconvolution">
+          <param name="charge_min" value="1"/>
+          <param name="charge_max" value="3"/>
+          <param name="charge_span_max" value="3"/>
+          <param name="q_try" value="feature"/>
+          <param name="retention_max_diff" value="1.0"/>
+          <param name="retention_max_diff_local" value="1.0"/>
+          <param name="mass_max_diff" value="0.05"/>
+          <param name="unit" value="Da"/>
+          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
+          <param name="max_neutrals" value="1"/>
+          <param name="use_minority_bound" value="true"/>
+          <param name="max_minority_bound" value="3"/>
+          <param name="min_rt_overlap" value="0.66"/>
+          <param name="intensity_filter" value="false"/>
+          <param name="negative_mode" value="false"/>
+          <param name="default_map_label" value="decharged features"/>
+          <param name="verbose_level" value="0"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
   <xml name="autotest_MetaboliteSpectralMatcher">
 </xml>
   <xml name="autotest_MetaProSIP">
@@ -16055,6 +16792,7 @@
     <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
+        <param name="add_decoys" value="false"/>
         <param name="legacy_conversion" value="false"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -16063,7 +16801,6 @@
       <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
       <param name="database" value="proteins.fasta"/>
-      <param name="add_decoys" value="false"/>
       <param name="precursor_mass_tolerance" value="10.0"/>
       <param name="precursor_error_units" value="ppm"/>
       <param name="isotope_error_range" value="0,1"/>
@@ -16079,6 +16816,8 @@
       <param name="matches_per_spec" value="1"/>
       <param name="add_features" value="false"/>
       <param name="max_mods" value="2"/>
+      <param name="max_missed_cleavages" value="-1"/>
+      <param name="tasks" value="0"/>
       <param name="fixed_modifications" value=""/>
       <param name="variable_modifications" value="Oxidation (M)"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
@@ -16413,6 +17152,74 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="Epifany_2_out.consensusXML"/>
+      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="true"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
+      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_6_input.idXML"/>
+      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="first_run_inference_only" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
+      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
+      <param name="opt_columns" value="subfeatures"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </xml>
   <xml name="autotest_NoiseFilterGaussian">
     <test expect_num_outputs="2">
@@ -16919,6 +17726,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17030,6 +17838,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17141,6 +17950,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17252,6 +18062,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17362,6 +18173,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17473,6 +18285,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17584,6 +18397,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17695,6 +18509,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -17806,6 +18621,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18290,6 +19106,8 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_OpenSwathDIAPreScoring">
+</xml>
   <xml name="autotest_OpenSwathFeatureXMLToTSV">
     <test expect_num_outputs="2">
       <conditional name="adv_opts_cond">
@@ -18594,6 +19412,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18715,6 +19534,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18836,6 +19656,7 @@
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="stop_after_intensity_ratio" value="0.0001"/>
@@ -18932,17 +19753,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -18951,10 +19772,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -18965,8 +19786,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -18994,7 +19815,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19008,10 +19829,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19023,7 +19845,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19067,13 +19889,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19089,17 +19911,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19108,10 +19930,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
       <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
@@ -19121,8 +19943,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19150,7 +19972,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19164,10 +19986,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19179,7 +20002,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19223,13 +20046,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19245,17 +20068,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19264,10 +20087,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19277,8 +20100,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19306,7 +20129,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19320,10 +20143,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19335,7 +20159,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19379,13 +20203,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19401,17 +20225,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19420,10 +20244,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19433,8 +20257,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19462,7 +20286,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19476,10 +20300,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19491,7 +20316,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19535,13 +20360,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19557,17 +20382,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19576,10 +20401,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19589,8 +20414,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19618,7 +20443,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19632,10 +20457,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19647,7 +20473,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19691,13 +20517,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19713,17 +20539,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19732,10 +20558,10 @@
         <param name="readOptions" value="cacheWorkingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -19745,8 +20571,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19774,7 +20600,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19788,10 +20614,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19803,7 +20630,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -19847,13 +20674,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -19868,19 +20695,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -19889,21 +20715,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -19931,7 +20758,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -19945,10 +20772,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -19960,7 +20788,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20004,13 +20832,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20025,19 +20853,18 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20046,21 +20873,22 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
         <param name="force" value="true"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
       <param name="tr_type" value=""/>
+      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
       <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
       <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20088,7 +20916,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20102,10 +20930,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20117,7 +20946,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20161,13 +20990,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20182,13 +21011,13 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="false"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="false"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
         <param name="irt_mz_extraction_window" value="550.0"/>
@@ -20201,10 +21030,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
@@ -20216,7 +21045,7 @@
       <param name="rt_extraction_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.2"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20244,7 +21073,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20258,10 +21087,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20273,7 +21103,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20317,13 +21147,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="true"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20339,17 +21169,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20358,10 +21188,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
@@ -20371,8 +21201,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20400,7 +21230,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20414,10 +21244,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20429,7 +21260,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20473,13 +21304,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20495,17 +21326,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="sqMass"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20514,10 +21345,10 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
@@ -20527,8 +21358,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20556,7 +21387,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20570,10 +21401,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20585,7 +21417,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20629,13 +21461,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20651,17 +21483,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20670,7 +21502,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -20684,7 +21516,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20712,7 +21544,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20726,10 +21558,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20807,17 +21640,17 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20826,10 +21659,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="2"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
       <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
@@ -20839,8 +21672,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -20868,7 +21701,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -20882,10 +21715,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -20897,7 +21731,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -20941,13 +21775,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -20962,17 +21796,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -20981,10 +21815,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -20994,8 +21828,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21023,7 +21857,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21037,10 +21871,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21052,7 +21887,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21096,13 +21931,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21117,17 +21952,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21136,10 +21971,10 @@
         <param name="readOptions" value="cache"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
@@ -21149,8 +21984,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21178,7 +22013,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21192,10 +22027,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21207,7 +22043,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21251,13 +22087,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="true"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21272,17 +22108,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="false"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21291,10 +22127,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="batchSize" value="1000"/>
+        <param name="ms1_isotopes" value="3"/>
+        <param name="force" value="false"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
@@ -21304,8 +22140,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21333,7 +22169,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21347,10 +22183,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21362,7 +22199,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -21406,13 +22243,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -21428,16 +22265,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21446,7 +22283,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21459,7 +22296,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21487,7 +22324,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21501,10 +22338,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21582,16 +22420,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21600,7 +22438,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21613,7 +22451,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21641,7 +22479,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21655,10 +22493,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21736,16 +22575,16 @@
         <param name="adv_opts_selector" value="advanced"/>
         <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21754,7 +22593,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21767,7 +22606,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -21795,7 +22634,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21809,10 +22648,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -21889,17 +22729,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
         <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -21908,7 +22748,7 @@
         <param name="readOptions" value="normal"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="0"/>
         <param name="force" value="false"/>
         <param name="test" value="true"/>
@@ -21923,7 +22763,7 @@
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
       <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
@@ -21952,7 +22792,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.6666666666666666"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -21966,10 +22806,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22046,17 +22887,17 @@
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="sort_swath_maps" value="false"/>
-        <param name="use_ms1_traces" value="true"/>
-        <param name="enable_uis_scoring" value="false"/>
+        <param name="enable_ms1" value="true"/>
+        <param name="enable_ipf" value="true"/>
         <param name="out_chrom_type" value="mzML"/>
         <param name="min_upper_edge_dist" value="0.0"/>
         <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="Th"/>
+        <param name="mz_extraction_window_unit" value="ppm"/>
+        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
         <param name="use_ms1_ion_mobility" value="true"/>
         <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="0.05"/>
-        <param name="irt_mz_extraction_window_unit" value="Th"/>
+        <param name="irt_mz_extraction_window" value="50.0"/>
+        <param name="irt_mz_extraction_window_unit" value="ppm"/>
         <param name="irt_im_extraction_window" value="-1.0"/>
         <param name="min_rsq" value="0.95"/>
         <param name="min_coverage" value="0.6"/>
@@ -22065,10 +22906,10 @@
         <param name="readOptions" value="workingInMemory"/>
         <param name="mz_correction_function" value="none"/>
         <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="250"/>
+        <param name="batchSize" value="1000"/>
         <param name="ms1_isotopes" value="3"/>
         <param name="force" value="false"/>
-        <param name="test" value="true"/>
+        <param name="test" value="false"/>
       </conditional>
       <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
       <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
@@ -22078,8 +22919,8 @@
       <param name="sonar" value="false"/>
       <param name="rt_extraction_window" value="600.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="0.05"/>
+      <param name="mz_extraction_window" value="50.0"/>
+      <param name="mz_extraction_window_ms1" value="50.0"/>
       <param name="im_extraction_window_ms1" value="-1.0"/>
       <section name="Debugging"/>
       <section name="Calibration">
@@ -22107,7 +22948,7 @@
         <param name="MinPeptidesPerBin" value="1"/>
         <param name="MinBinsFilled" value="8"/>
         <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
+          <param name="span" value="0.05"/>
         </section>
         <section name="b_spline">
           <param name="num_nodes" value="5"/>
@@ -22121,10 +22962,11 @@
         <param name="spectrum_addition_method" value="simple"/>
         <param name="add_up_spectra" value="1"/>
         <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="0"/>
+        <param name="uis_threshold_sn" value="-1"/>
         <param name="uis_threshold_peak_area" value="0"/>
         <param name="scoring_model" value="default"/>
         <param name="im_extra_drift" value="0.0"/>
+        <param name="strict" value="true"/>
         <section name="TransitionGroupPicker">
           <param name="stop_after_feature" value="-1"/>
           <param name="min_peak_width" value="-1.0"/>
@@ -22136,7 +22978,7 @@
           <param name="recalculate_peaks_max_z" value="0.75"/>
           <param name="minimal_quality" value="-1.5"/>
           <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
+          <param name="compute_peak_quality" value="false"/>
           <param name="compute_peak_shape_metrics" value="false"/>
           <param name="compute_total_mi" value="false"/>
           <param name="boundary_selection_method" value="largest"/>
@@ -22180,13 +23022,13 @@
           <param name="use_total_xic_score" value="true"/>
           <param name="use_total_mi_score" value="false"/>
           <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
+          <param name="use_mi_score" value="true"/>
           <param name="use_dia_scores" value="true"/>
           <param name="use_ms1_correlation" value="false"/>
           <param name="use_sonar_scores" value="false"/>
           <param name="use_ion_mobility_scores" value="false"/>
           <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
+          <param name="use_ms1_mi" value="true"/>
           <param name="use_uis_scores" value="false"/>
         </section>
       </section>
@@ -22207,7 +23049,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
+      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise" value="1.0"/>
         <param name="spacing_difference_gap" value="4.0"/>
@@ -22762,12 +23604,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22792,12 +23634,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22822,12 +23664,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="true"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22852,12 +23694,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="0"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22882,12 +23724,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22912,12 +23754,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22942,12 +23784,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="full"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -22972,12 +23814,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="semi"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23002,12 +23844,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="remove"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23032,13 +23874,13 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="3"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="true"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23062,12 +23904,12 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="true"/>
+      <param name="unmatched_action" value="warn"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23092,13 +23934,13 @@
       <param name="write_protein_sequence" value="false"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
-        <param name="specificity" value="full"/>
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -23122,12 +23964,12 @@
       <param name="write_protein_sequence" value="true"/>
       <param name="write_protein_description" value="false"/>
       <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="allow_unmatched" value="false"/>
+      <param name="unmatched_action" value="error"/>
       <param name="aaa_max" value="4"/>
       <param name="mismatches_max" value="0"/>
       <param name="IL_equivalent" value="false"/>
       <section name="enzyme">
-        <param name="name" value="Trypsin"/>
+        <param name="name" value="auto"/>
         <param name="specificity" value="none"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -23149,7 +23991,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23192,7 +24036,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23235,7 +24081,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23278,7 +24126,9 @@
         <param name="testFDR" value="0.01"/>
         <param name="trainFDR" value="0.01"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23321,7 +24171,9 @@
         <param name="testFDR" value="0.5"/>
         <param name="trainFDR" value="0.5"/>
         <param name="maxiter" value="10"/>
+        <param name="nested_xval_bins" value="1"/>
         <param name="quick_validation" value="false"/>
+        <param name="static" value="false"/>
         <param name="default_direction" value=""/>
         <param name="verbose" value="2"/>
         <param name="unitnorm" value="false"/>
@@ -23539,6 +24391,7 @@
       <param name="annotate_indist_groups" value="true"/>
       <section name="Merging">
         <param name="annotate_origin" value="false"/>
+        <param name="allow_disagreeing_settings" value="false"/>
       </section>
       <section name="Algorithm">
         <param name="min_peptides_per_protein" value="1"/>
@@ -23808,7 +24661,7 @@
         </assert_contents>
       </output>
     </test>
-    <test expect_num_outputs="2">
+    <test expect_num_outputs="3">
       <conditional name="adv_opts_cond">
         <param name="adv_opts_selector" value="advanced"/>
         <param name="force" value="false"/>
@@ -23816,6 +24669,7 @@
       </conditional>
       <param name="in" value="ProteinQuantifier_input.consensusXML"/>
       <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
       <param name="top" value="3"/>
       <param name="average" value="sum"/>
       <param name="include_all" value="true"/>
@@ -23832,7 +24686,7 @@
         <param name="quoting" value="double"/>
         <param name="replacement" value="_"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24047,9 +24901,9 @@
         <param name="tolerance" value="20.0"/>
       </section>
       <section name="MS2_id_rate">
-        <param name="force_no_fdr" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/>
+        <param name="assume_all_target" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -24570,6 +25424,7 @@
       <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
       <section name="Search">
         <param name="enzyme" value="Trypsin"/>
+        <param name="decoys" value="false"/>
         <section name="precursor">
           <param name="mass_tolerance" value="5.0"/>
           <param name="mass_tolerance_unit" value="ppm"/>
@@ -24586,6 +25441,9 @@
           <param name="variable" value="Oxidation (M)"/>
           <param name="variable_max_per_peptide" value="2"/>
         </section>
+        <section name="annotate">
+          <param name="PSM" value=""/>
+        </section>
         <section name="peptide">
           <param name="min_size" value="7"/>
           <param name="max_size" value="40"/>
@@ -24635,7 +25493,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24679,7 +25536,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24723,7 +25579,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -24767,7 +25622,6 @@
         <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"/>
@@ -24811,7 +25665,6 @@
         <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"/>
@@ -24855,7 +25708,6 @@
         <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"/>
@@ -24892,7 +25744,7 @@
       <section name="sirius">
         <param name="profile" value="qtof"/>
         <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
+        <param name="database" value="pubchem"/>
         <param name="noise" value="0"/>
         <param name="ppm_max" value="10"/>
         <param name="isotope" value="both"/>
@@ -24900,7 +25752,6 @@
         <param name="compound_timeout" value="10"/>
         <param name="tree_timeout" value="0"/>
         <param name="top_n_hits" value="10"/>
-        <param name="cores" value="1"/>
         <param name="auto_charge" value="true"/>
         <param name="ion_tree" value="false"/>
         <param name="no_recalibration" value="false"/>
@@ -25035,6 +25886,8 @@
   <xml name="autotest_SpectraMerger">
 </xml>
   <xml name="autotest_SpectraSTSearchAdapter"/>
+  <xml name="autotest_StaticModification">
+</xml>
   <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
 </xml>
   <xml name="autotest_TargetedFileConverter">
@@ -25487,7 +26340,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25510,7 +26363,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25524,7 +26377,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25550,7 +26403,7 @@
       <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
       <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25564,7 +26417,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25587,7 +26440,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25601,7 +26454,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25624,7 +26477,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25638,7 +26491,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25661,7 +26514,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25675,7 +26528,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25698,7 +26551,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25712,7 +26565,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25735,7 +26588,7 @@
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25749,7 +26602,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25772,7 +26625,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25786,7 +26639,7 @@
         <param name="test" value="true"/>
       </conditional>
       <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
+      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
       <param name="separator" value=""/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -25809,7 +26662,7 @@
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
       </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
@@ -25909,8 +26762,8 @@
       <param name="in" value="TOFCalibration_1_input.mzML"/>
       <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="false"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -25991,8 +26844,8 @@
       <param name="in" value="TOFCalibration_2_input.mzML"/>
       <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
       <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
-      <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
+      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
+      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
       <param name="peak_data" value="true"/>
       <section name="algorithm">
         <section name="PeakPicker">
@@ -26316,5 +27169,37 @@
         </assert_contents>
       </output>
     </test>
-  </xml>
-<xml name="autotest_InspectAdapter"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_RTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_DigestorMotif"/><xml name="autotest_PTPredict"/></macros>
+    <test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="spectra.mzML"/>
+      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="proteinslong.fasta"/>
+      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
+      <param name="ignore_adapter_param" value="false"/>
+      <param name="precursor_mass_tolerance" value="5.0"/>
+      <param name="fragment_mass_tolerance" value="0.3"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="fragment_error_units" value="Da"/>
+      <param name="max_precursor_charge" value="0"/>
+      <param name="no_isotope_error" value="false"/>
+      <param name="fixed_modifications" value=""/>
+      <param name="variable_modifications" value="Oxidation (M)"/>
+      <param name="minimum_fragment_mz" value="150.0"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="missed_cleavages" value="1"/>
+      <param name="semi_cleavage" value="false"/>
+      <param name="output_results" value="all"/>
+      <param name="max_valid_expect" value="0.1"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+  </xml>
+<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>