Mercurial > repos > galaxyp > openms_openswathanalyzer
diff macros_autotest.xml @ 11:7ca917175b23 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 19:43:44 +0000 |
| parents | 4da16805dea6 |
| children |
line wrap: on
line diff
--- a/macros_autotest.xml Thu Sep 24 12:33:57 2020 +0000 +++ b/macros_autotest.xml Tue Oct 13 19:43:44 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=""Q9HP81""/> + <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=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> - <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=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> + <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=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> + <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>