Mercurial > repos > galaxyp > openms_idmapper

comparison macros_autotest.xml @ 13:2517c03f5cd3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:04:21 +0000
parents 0bdaa74d9a3a
children
comparison
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12:0bdaa74d9a3a 13:2517c03f5cd3
156 <param name="isotope" value="both"/> 156 <param name="isotope" value="both"/>
157 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 157 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
158 <param name="compound_timeout" value="10"/> 158 <param name="compound_timeout" value="10"/>
159 <param name="tree_timeout" value="0"/> 159 <param name="tree_timeout" value="0"/>
160 <param name="top_n_hits" value="10"/> 160 <param name="top_n_hits" value="10"/>
161 <param name="cores" value="1"/>
162 <param name="auto_charge" value="false"/> 161 <param name="auto_charge" value="false"/>
163 <param name="ion_tree" value="false"/> 162 <param name="ion_tree" value="false"/>
164 <param name="no_recalibration" value="false"/> 163 <param name="no_recalibration" value="false"/>
165 <param name="most_intense_ms2" value="false"/> 164 <param name="most_intense_ms2" value="false"/>
166 </section> 165 </section>
226 <param name="isotope" value="both"/> 225 <param name="isotope" value="both"/>
227 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 226 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
228 <param name="compound_timeout" value="10"/> 227 <param name="compound_timeout" value="10"/>
229 <param name="tree_timeout" value="0"/> 228 <param name="tree_timeout" value="0"/>
230 <param name="top_n_hits" value="10"/> 229 <param name="top_n_hits" value="10"/>
231 <param name="cores" value="1"/>
232 <param name="auto_charge" value="false"/> 230 <param name="auto_charge" value="false"/>
233 <param name="ion_tree" value="false"/> 231 <param name="ion_tree" value="false"/>
234 <param name="no_recalibration" value="false"/> 232 <param name="no_recalibration" value="false"/>
235 <param name="most_intense_ms2" value="false"/> 233 <param name="most_intense_ms2" value="false"/>
236 </section> 234 </section>
296 <param name="isotope" value="both"/> 294 <param name="isotope" value="both"/>
297 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 295 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
298 <param name="compound_timeout" value="10"/> 296 <param name="compound_timeout" value="10"/>
299 <param name="tree_timeout" value="0"/> 297 <param name="tree_timeout" value="0"/>
300 <param name="top_n_hits" value="10"/> 298 <param name="top_n_hits" value="10"/>
301 <param name="cores" value="1"/>
302 <param name="auto_charge" value="false"/> 299 <param name="auto_charge" value="false"/>
303 <param name="ion_tree" value="false"/> 300 <param name="ion_tree" value="false"/>
304 <param name="no_recalibration" value="false"/> 301 <param name="no_recalibration" value="false"/>
305 <param name="most_intense_ms2" value="false"/> 302 <param name="most_intense_ms2" value="false"/>
306 </section> 303 </section>
366 <param name="isotope" value="both"/> 363 <param name="isotope" value="both"/>
367 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 364 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
368 <param name="compound_timeout" value="10"/> 365 <param name="compound_timeout" value="10"/>
369 <param name="tree_timeout" value="0"/> 366 <param name="tree_timeout" value="0"/>
370 <param name="top_n_hits" value="10"/> 367 <param name="top_n_hits" value="10"/>
371 <param name="cores" value="1"/>
372 <param name="auto_charge" value="false"/> 368 <param name="auto_charge" value="false"/>
373 <param name="ion_tree" value="false"/> 369 <param name="ion_tree" value="false"/>
374 <param name="no_recalibration" value="false"/> 370 <param name="no_recalibration" value="false"/>
375 <param name="most_intense_ms2" value="false"/> 371 <param name="most_intense_ms2" value="false"/>
376 </section> 372 </section>
436 <param name="isotope" value="both"/> 432 <param name="isotope" value="both"/>
437 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 433 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
438 <param name="compound_timeout" value="10"/> 434 <param name="compound_timeout" value="10"/>
439 <param name="tree_timeout" value="0"/> 435 <param name="tree_timeout" value="0"/>
440 <param name="top_n_hits" value="10"/> 436 <param name="top_n_hits" value="10"/>
441 <param name="cores" value="1"/>
442 <param name="auto_charge" value="false"/> 437 <param name="auto_charge" value="false"/>
443 <param name="ion_tree" value="false"/> 438 <param name="ion_tree" value="false"/>
444 <param name="no_recalibration" value="false"/> 439 <param name="no_recalibration" value="false"/>
445 <param name="most_intense_ms2" value="false"/> 440 <param name="most_intense_ms2" value="false"/>
446 </section> 441 </section>
506 <param name="isotope" value="both"/> 501 <param name="isotope" value="both"/>
507 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 502 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
508 <param name="compound_timeout" value="100"/> 503 <param name="compound_timeout" value="100"/>
509 <param name="tree_timeout" value="0"/> 504 <param name="tree_timeout" value="0"/>
510 <param name="top_n_hits" value="10"/> 505 <param name="top_n_hits" value="10"/>
511 <param name="cores" value="1"/>
512 <param name="auto_charge" value="false"/> 506 <param name="auto_charge" value="false"/>
513 <param name="ion_tree" value="false"/> 507 <param name="ion_tree" value="false"/>
514 <param name="no_recalibration" value="false"/> 508 <param name="no_recalibration" value="false"/>
515 <param name="most_intense_ms2" value="false"/> 509 <param name="most_intense_ms2" value="false"/>
516 </section> 510 </section>
576 <param name="isotope" value="both"/> 570 <param name="isotope" value="both"/>
577 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 571 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
578 <param name="compound_timeout" value="100"/> 572 <param name="compound_timeout" value="100"/>
579 <param name="tree_timeout" value="0"/> 573 <param name="tree_timeout" value="0"/>
580 <param name="top_n_hits" value="10"/> 574 <param name="top_n_hits" value="10"/>
581 <param name="cores" value="1"/>
582 <param name="auto_charge" value="false"/> 575 <param name="auto_charge" value="false"/>
583 <param name="ion_tree" value="false"/> 576 <param name="ion_tree" value="false"/>
584 <param name="no_recalibration" value="false"/> 577 <param name="no_recalibration" value="false"/>
585 <param name="most_intense_ms2" value="false"/> 578 <param name="most_intense_ms2" value="false"/>
586 </section> 579 </section>
646 <param name="isotope" value="both"/> 639 <param name="isotope" value="both"/>
647 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 640 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
648 <param name="compound_timeout" value="100"/> 641 <param name="compound_timeout" value="100"/>
649 <param name="tree_timeout" value="0"/> 642 <param name="tree_timeout" value="0"/>
650 <param name="top_n_hits" value="10"/> 643 <param name="top_n_hits" value="10"/>
651 <param name="cores" value="1"/>
652 <param name="auto_charge" value="false"/> 644 <param name="auto_charge" value="false"/>
653 <param name="ion_tree" value="false"/> 645 <param name="ion_tree" value="false"/>
654 <param name="no_recalibration" value="false"/> 646 <param name="no_recalibration" value="false"/>
655 <param name="most_intense_ms2" value="false"/> 647 <param name="most_intense_ms2" value="false"/>
656 </section> 648 </section>
716 <param name="isotope" value="both"/> 708 <param name="isotope" value="both"/>
717 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 709 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
718 <param name="compound_timeout" value="100"/> 710 <param name="compound_timeout" value="100"/>
719 <param name="tree_timeout" value="0"/> 711 <param name="tree_timeout" value="0"/>
720 <param name="top_n_hits" value="10"/> 712 <param name="top_n_hits" value="10"/>
721 <param name="cores" value="1"/>
722 <param name="auto_charge" value="false"/> 713 <param name="auto_charge" value="false"/>
723 <param name="ion_tree" value="false"/> 714 <param name="ion_tree" value="false"/>
724 <param name="no_recalibration" value="false"/> 715 <param name="no_recalibration" value="false"/>
725 <param name="most_intense_ms2" value="false"/> 716 <param name="most_intense_ms2" value="false"/>
726 </section> 717 </section>
758 </xml> 749 </xml>
759 <xml name="autotest_CometAdapter"> 750 <xml name="autotest_CometAdapter">
760 <test expect_num_outputs="3"> 751 <test expect_num_outputs="3">
761 <conditional name="adv_opts_cond"> 752 <conditional name="adv_opts_cond">
762 <param name="adv_opts_selector" value="advanced"/> 753 <param name="adv_opts_selector" value="advanced"/>
763 <param name="fragment_bin_tolerance" value="1.0005"/>
764 <param name="fragment_bin_offset" value="0.25"/>
765 <param name="instrument" value="high_res"/>
766 <param name="use_A_ions" value="false"/> 754 <param name="use_A_ions" value="false"/>
767 <param name="use_B_ions" value="true"/> 755 <param name="use_B_ions" value="true"/>
768 <param name="use_C_ions" value="false"/> 756 <param name="use_C_ions" value="false"/>
769 <param name="use_X_ions" value="false"/> 757 <param name="use_X_ions" value="false"/>
770 <param name="use_Y_ions" value="true"/> 758 <param name="use_Y_ions" value="true"/>
771 <param name="use_Z_ions" value="false"/> 759 <param name="use_Z_ions" value="false"/>
772 <param name="use_NL_ions" value="false"/> 760 <param name="use_NL_ions" value="false"/>
761 <param name="second_enzyme" value=""/>
773 <param name="digest_mass_range" value="600:5000"/> 762 <param name="digest_mass_range" value="600:5000"/>
774 <param name="max_precursor_charge" value="5"/> 763 <param name="max_precursor_charge" value="5"/>
775 <param name="spectrum_batch_size" value="1000"/> 764 <param name="spectrum_batch_size" value="1000"/>
776 <param name="mass_offsets" value="0.0"/> 765 <param name="mass_offsets" value="0.0"/>
777 <param name="minimum_peaks" value="10"/> 766 <param name="minimum_peaks" value="10"/>
779 <param name="remove_precursor_peak" value="no"/> 768 <param name="remove_precursor_peak" value="no"/>
780 <param name="remove_precursor_tolerance" value="1.5"/> 769 <param name="remove_precursor_tolerance" value="1.5"/>
781 <param name="clear_mz_range" value="0:0"/> 770 <param name="clear_mz_range" value="0:0"/>
782 <param name="max_variable_mods_in_peptide" value="5"/> 771 <param name="max_variable_mods_in_peptide" value="5"/>
783 <param name="require_variable_mod" value="false"/> 772 <param name="require_variable_mod" value="false"/>
784 <param name="force" value="false"/> 773 <param name="force" value="true"/>
785 <param name="test" value="true"/> 774 <param name="test" value="true"/>
786 </conditional> 775 </conditional>
787 <param name="in" value="spectra_comet.mzML"/> 776 <param name="in" value="spectra_comet.mzML"/>
788 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 777 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
789 <param name="database" value="proteins.fasta"/> 778 <param name="database" value="proteins.fasta"/>
790 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> 779 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
791 <param name="precursor_mass_tolerance" value="3.0"/> 780 <param name="precursor_mass_tolerance" value="3.0"/>
792 <param name="precursor_error_units" value="ppm"/> 781 <param name="precursor_error_units" value="ppm"/>
793 <param name="isotope_error" value="off"/> 782 <param name="isotope_error" value="off"/>
783 <param name="fragment_mass_tolerance" value="0.50025"/>
784 <param name="fragment_error_units" value="Da"/>
785 <param name="fragment_bin_offset" value="0.25"/>
786 <param name="instrument" value="high_res"/>
794 <param name="enzyme" value="Trypsin"/> 787 <param name="enzyme" value="Trypsin"/>
795 <param name="num_enzyme_termini" value="fully"/> 788 <param name="num_enzyme_termini" value="fully"/>
796 <param name="allowed_missed_cleavages" value="1"/> 789 <param name="missed_cleavages" value="1"/>
790 <param name="min_peptide_length" value="5"/>
791 <param name="max_peptide_length" value="63"/>
797 <param name="num_hits" value="5"/> 792 <param name="num_hits" value="5"/>
798 <param name="precursor_charge" value="0:0"/> 793 <param name="precursor_charge" value="0:0"/>
799 <param name="override_charge" value="keep any known"/> 794 <param name="override_charge" value="keep any known"/>
800 <param name="ms_level" value="2"/> 795 <param name="ms_level" value="2"/>
801 <param name="activation_method" value="ALL"/> 796 <param name="activation_method" value="ALL"/>
802 <param name="max_fragment_charge" value="3"/> 797 <param name="max_fragment_charge" value="3"/>
803 <param name="clip_nterm_methionine" value="false"/> 798 <param name="clip_nterm_methionine" value="false"/>
804 <param name="fixed_modifications" value=""/> 799 <param name="fixed_modifications" value=""/>
805 <param name="variable_modifications" value=""/> 800 <param name="variable_modifications" value=""/>
801 <param name="binary_modifications" value=""/>
806 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> 802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
807 <output name="ctd_out" ftype="xml"> 803 <output name="ctd_out" ftype="xml">
808 <assert_contents> 804 <assert_contents>
809 <is_valid_xml/> 805 <is_valid_xml/>
810 </assert_contents> 806 </assert_contents>
811 </output> 807 </output>
812 </test> 808 </test>
813 <test expect_num_outputs="3"> 809 <test expect_num_outputs="3">
814 <conditional name="adv_opts_cond"> 810 <conditional name="adv_opts_cond">
815 <param name="adv_opts_selector" value="advanced"/> 811 <param name="adv_opts_selector" value="advanced"/>
816 <param name="fragment_bin_tolerance" value="1.0005"/>
817 <param name="fragment_bin_offset" value="0.25"/>
818 <param name="instrument" value="high_res"/>
819 <param name="use_A_ions" value="false"/> 812 <param name="use_A_ions" value="false"/>
820 <param name="use_B_ions" value="true"/> 813 <param name="use_B_ions" value="true"/>
821 <param name="use_C_ions" value="false"/> 814 <param name="use_C_ions" value="false"/>
822 <param name="use_X_ions" value="false"/> 815 <param name="use_X_ions" value="false"/>
823 <param name="use_Y_ions" value="true"/> 816 <param name="use_Y_ions" value="true"/>
824 <param name="use_Z_ions" value="false"/> 817 <param name="use_Z_ions" value="false"/>
825 <param name="use_NL_ions" value="false"/> 818 <param name="use_NL_ions" value="false"/>
819 <param name="second_enzyme" value=""/>
826 <param name="digest_mass_range" value="600:5000"/> 820 <param name="digest_mass_range" value="600:5000"/>
827 <param name="max_precursor_charge" value="5"/> 821 <param name="max_precursor_charge" value="5"/>
828 <param name="spectrum_batch_size" value="1000"/> 822 <param name="spectrum_batch_size" value="1000"/>
829 <param name="mass_offsets" value="0.0"/> 823 <param name="mass_offsets" value="0.0"/>
830 <param name="minimum_peaks" value="10"/> 824 <param name="minimum_peaks" value="10"/>
832 <param name="remove_precursor_peak" value="no"/> 826 <param name="remove_precursor_peak" value="no"/>
833 <param name="remove_precursor_tolerance" value="1.5"/> 827 <param name="remove_precursor_tolerance" value="1.5"/>
834 <param name="clear_mz_range" value="0:0"/> 828 <param name="clear_mz_range" value="0:0"/>
835 <param name="max_variable_mods_in_peptide" value="5"/> 829 <param name="max_variable_mods_in_peptide" value="5"/>
836 <param name="require_variable_mod" value="false"/> 830 <param name="require_variable_mod" value="false"/>
837 <param name="force" value="false"/> 831 <param name="force" value="true"/>
838 <param name="test" value="true"/> 832 <param name="test" value="true"/>
839 </conditional> 833 </conditional>
840 <param name="in" value="CometAdapter_2_prepared.mzML"/> 834 <param name="in" value="CometAdapter_2_prepared.mzML"/>
841 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 835 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
842 <param name="database" value="CometAdapter_2_in.fasta"/> 836 <param name="database" value="CometAdapter_2_in.fasta"/>
843 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> 837 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
844 <param name="precursor_mass_tolerance" value="3.0"/> 838 <param name="precursor_mass_tolerance" value="3.0"/>
845 <param name="precursor_error_units" value="Da"/> 839 <param name="precursor_error_units" value="Da"/>
846 <param name="isotope_error" value="off"/> 840 <param name="isotope_error" value="off"/>
841 <param name="fragment_mass_tolerance" value="0.50025"/>
842 <param name="fragment_error_units" value="Da"/>
843 <param name="fragment_bin_offset" value="0.25"/>
844 <param name="instrument" value="high_res"/>
847 <param name="enzyme" value="Trypsin"/> 845 <param name="enzyme" value="Trypsin"/>
848 <param name="num_enzyme_termini" value="fully"/> 846 <param name="num_enzyme_termini" value="fully"/>
849 <param name="allowed_missed_cleavages" value="1"/> 847 <param name="missed_cleavages" value="1"/>
848 <param name="min_peptide_length" value="5"/>
849 <param name="max_peptide_length" value="63"/>
850 <param name="num_hits" value="5"/> 850 <param name="num_hits" value="5"/>
851 <param name="precursor_charge" value="0:0"/> 851 <param name="precursor_charge" value="0:0"/>
852 <param name="override_charge" value="keep any known"/> 852 <param name="override_charge" value="keep any known"/>
853 <param name="ms_level" value="2"/> 853 <param name="ms_level" value="2"/>
854 <param name="activation_method" value="ALL"/> 854 <param name="activation_method" value="ALL"/>
855 <param name="max_fragment_charge" value="3"/> 855 <param name="max_fragment_charge" value="3"/>
856 <param name="clip_nterm_methionine" value="false"/> 856 <param name="clip_nterm_methionine" value="false"/>
857 <param name="fixed_modifications" value=""/> 857 <param name="fixed_modifications" value=""/>
858 <param name="variable_modifications" value=""/> 858 <param name="variable_modifications" value=""/>
859 <param name="binary_modifications" value=""/>
859 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> 860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
860 <output name="ctd_out" ftype="xml"> 861 <output name="ctd_out" ftype="xml">
861 <assert_contents> 862 <assert_contents>
862 <is_valid_xml/> 863 <is_valid_xml/>
863 </assert_contents> 864 </assert_contents>
864 </output> 865 </output>
865 </test> 866 </test>
866 <test expect_num_outputs="3"> 867 <test expect_num_outputs="3">
867 <conditional name="adv_opts_cond"> 868 <conditional name="adv_opts_cond">
868 <param name="adv_opts_selector" value="advanced"/> 869 <param name="adv_opts_selector" value="advanced"/>
869 <param name="fragment_bin_tolerance" value="0.02"/>
870 <param name="fragment_bin_offset" value="0.0"/>
871 <param name="instrument" value="high_res"/>
872 <param name="use_A_ions" value="false"/> 870 <param name="use_A_ions" value="false"/>
873 <param name="use_B_ions" value="true"/> 871 <param name="use_B_ions" value="true"/>
874 <param name="use_C_ions" value="false"/> 872 <param name="use_C_ions" value="false"/>
875 <param name="use_X_ions" value="false"/> 873 <param name="use_X_ions" value="false"/>
876 <param name="use_Y_ions" value="true"/> 874 <param name="use_Y_ions" value="true"/>
877 <param name="use_Z_ions" value="false"/> 875 <param name="use_Z_ions" value="false"/>
878 <param name="use_NL_ions" value="false"/> 876 <param name="use_NL_ions" value="false"/>
877 <param name="second_enzyme" value=""/>
879 <param name="digest_mass_range" value="600:5000"/> 878 <param name="digest_mass_range" value="600:5000"/>
880 <param name="max_precursor_charge" value="5"/> 879 <param name="max_precursor_charge" value="5"/>
881 <param name="spectrum_batch_size" value="20000"/> 880 <param name="spectrum_batch_size" value="20000"/>
882 <param name="mass_offsets" value="0.0"/> 881 <param name="mass_offsets" value="0.0"/>
883 <param name="minimum_peaks" value="10"/> 882 <param name="minimum_peaks" value="10"/>
895 <param name="database" value="CometAdapter_3.fasta"/> 894 <param name="database" value="CometAdapter_3.fasta"/>
896 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> 895 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
897 <param name="precursor_mass_tolerance" value="5.0"/> 896 <param name="precursor_mass_tolerance" value="5.0"/>
898 <param name="precursor_error_units" value="ppm"/> 897 <param name="precursor_error_units" value="ppm"/>
899 <param name="isotope_error" value="off"/> 898 <param name="isotope_error" value="off"/>
899 <param name="fragment_mass_tolerance" value="0.01"/>
900 <param name="fragment_error_units" value="Da"/>
901 <param name="fragment_bin_offset" value="0.0"/>
902 <param name="instrument" value="high_res"/>
900 <param name="enzyme" value="Trypsin"/> 903 <param name="enzyme" value="Trypsin"/>
901 <param name="num_enzyme_termini" value="fully"/> 904 <param name="num_enzyme_termini" value="fully"/>
902 <param name="allowed_missed_cleavages" value="3"/> 905 <param name="missed_cleavages" value="3"/>
906 <param name="min_peptide_length" value="5"/>
907 <param name="max_peptide_length" value="63"/>
903 <param name="num_hits" value="5"/> 908 <param name="num_hits" value="5"/>
904 <param name="precursor_charge" value="0:0"/> 909 <param name="precursor_charge" value="0:0"/>
905 <param name="override_charge" value="keep known search unknown"/> 910 <param name="override_charge" value="keep known search unknown"/>
906 <param name="ms_level" value="2"/> 911 <param name="ms_level" value="2"/>
907 <param name="activation_method" value="ALL"/> 912 <param name="activation_method" value="ALL"/>
908 <param name="max_fragment_charge" value="3"/> 913 <param name="max_fragment_charge" value="3"/>
909 <param name="clip_nterm_methionine" value="false"/> 914 <param name="clip_nterm_methionine" value="false"/>
910 <param name="fixed_modifications" value="Carbamidomethyl (C)"/> 915 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
911 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> 916 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
917 <param name="binary_modifications" value=""/>
912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> 918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
919 <output name="ctd_out" ftype="xml">
920 <assert_contents>
921 <is_valid_xml/>
922 </assert_contents>
923 </output>
924 </test>
925 <test expect_num_outputs="2">
926 <conditional name="adv_opts_cond">
927 <param name="adv_opts_selector" value="advanced"/>
928 <param name="use_A_ions" value="false"/>
929 <param name="use_B_ions" value="true"/>
930 <param name="use_C_ions" value="false"/>
931 <param name="use_X_ions" value="false"/>
932 <param name="use_Y_ions" value="true"/>
933 <param name="use_Z_ions" value="false"/>
934 <param name="use_NL_ions" value="false"/>
935 <param name="second_enzyme" value=""/>
936 <param name="digest_mass_range" value="600:1200"/>
937 <param name="max_precursor_charge" value="5"/>
938 <param name="spectrum_batch_size" value="20000"/>
939 <param name="mass_offsets" value="0.0"/>
940 <param name="minimum_peaks" value="10"/>
941 <param name="minimum_intensity" value="0.0"/>
942 <param name="remove_precursor_peak" value="no"/>
943 <param name="remove_precursor_tolerance" value="1.5"/>
944 <param name="clear_mz_range" value="0:0"/>
945 <param name="max_variable_mods_in_peptide" value="3"/>
946 <param name="require_variable_mod" value="false"/>
947 <param name="force" value="false"/>
948 <param name="test" value="true"/>
949 </conditional>
950 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
951 <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
952 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
953 <param name="precursor_mass_tolerance" value="5.0"/>
954 <param name="precursor_error_units" value="ppm"/>
955 <param name="isotope_error" value="off"/>
956 <param name="fragment_mass_tolerance" value="0.01"/>
957 <param name="fragment_error_units" value="Da"/>
958 <param name="fragment_bin_offset" value="0.0"/>
959 <param name="instrument" value="high_res"/>
960 <param name="enzyme" value="Trypsin"/>
961 <param name="num_enzyme_termini" value="fully"/>
962 <param name="missed_cleavages" value="3"/>
963 <param name="min_peptide_length" value="5"/>
964 <param name="max_peptide_length" value="63"/>
965 <param name="num_hits" value="5"/>
966 <param name="precursor_charge" value="0:0"/>
967 <param name="override_charge" value="keep known search unknown"/>
968 <param name="ms_level" value="2"/>
969 <param name="activation_method" value="ALL"/>
970 <param name="max_fragment_charge" value="3"/>
971 <param name="clip_nterm_methionine" value="false"/>
972 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
973 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
974 <param name="binary_modifications" value=""/>
975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
913 <output name="ctd_out" ftype="xml"> 976 <output name="ctd_out" ftype="xml">
914 <assert_contents> 977 <assert_contents>
915 <is_valid_xml/> 978 <is_valid_xml/>
916 </assert_contents> 979 </assert_contents>
917 </output> 980 </output>
1004 </conditional> 1067 </conditional>
1005 <param name="in" value="ConsensusID_1_input.idXML"/> 1068 <param name="in" value="ConsensusID_1_input.idXML"/>
1006 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 1069 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1007 <param name="rt_delta" value="0.1"/> 1070 <param name="rt_delta" value="0.1"/>
1008 <param name="mz_delta" value="0.1"/> 1071 <param name="mz_delta" value="0.1"/>
1072 <param name="per_spectrum" value="false"/>
1009 <param name="algorithm" value="PEPMatrix"/> 1073 <param name="algorithm" value="PEPMatrix"/>
1010 <section name="filter"> 1074 <section name="filter">
1011 <param name="considered_hits" value="0"/> 1075 <param name="considered_hits" value="0"/>
1012 <param name="min_support" value="0.0"/> 1076 <param name="min_support" value="0.0"/>
1013 <param name="count_empty" value="false"/> 1077 <param name="count_empty" value="false"/>
1078 <param name="keep_old_scores" value="false"/>
1014 </section> 1079 </section>
1015 <section name="PEPIons"> 1080 <section name="PEPIons">
1016 <param name="mass_tolerance" value="0.5"/> 1081 <param name="mass_tolerance" value="0.5"/>
1017 <param name="min_shared" value="2"/> 1082 <param name="min_shared" value="2"/>
1018 </section> 1083 </section>
1035 </conditional> 1100 </conditional>
1036 <param name="in" value="ConsensusID_2_input.featureXML"/> 1101 <param name="in" value="ConsensusID_2_input.featureXML"/>
1037 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> 1102 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1038 <param name="rt_delta" value="0.1"/> 1103 <param name="rt_delta" value="0.1"/>
1039 <param name="mz_delta" value="0.1"/> 1104 <param name="mz_delta" value="0.1"/>
1105 <param name="per_spectrum" value="false"/>
1040 <param name="algorithm" value="average"/> 1106 <param name="algorithm" value="average"/>
1041 <section name="filter"> 1107 <section name="filter">
1042 <param name="considered_hits" value="0"/> 1108 <param name="considered_hits" value="0"/>
1043 <param name="min_support" value="0.0"/> 1109 <param name="min_support" value="0.0"/>
1044 <param name="count_empty" value="false"/> 1110 <param name="count_empty" value="false"/>
1111 <param name="keep_old_scores" value="false"/>
1045 </section> 1112 </section>
1046 <section name="PEPIons"> 1113 <section name="PEPIons">
1047 <param name="mass_tolerance" value="0.5"/> 1114 <param name="mass_tolerance" value="0.5"/>
1048 <param name="min_shared" value="2"/> 1115 <param name="min_shared" value="2"/>
1049 </section> 1116 </section>
1066 </conditional> 1133 </conditional>
1067 <param name="in" value="ConsensusID_3_input.consensusXML"/> 1134 <param name="in" value="ConsensusID_3_input.consensusXML"/>
1068 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> 1135 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1069 <param name="rt_delta" value="0.1"/> 1136 <param name="rt_delta" value="0.1"/>
1070 <param name="mz_delta" value="0.1"/> 1137 <param name="mz_delta" value="0.1"/>
1138 <param name="per_spectrum" value="false"/>
1071 <param name="algorithm" value="best"/> 1139 <param name="algorithm" value="best"/>
1072 <section name="filter"> 1140 <section name="filter">
1073 <param name="considered_hits" value="0"/> 1141 <param name="considered_hits" value="0"/>
1074 <param name="min_support" value="0.0"/> 1142 <param name="min_support" value="0.0"/>
1075 <param name="count_empty" value="false"/> 1143 <param name="count_empty" value="false"/>
1144 <param name="keep_old_scores" value="false"/>
1076 </section> 1145 </section>
1077 <section name="PEPIons"> 1146 <section name="PEPIons">
1078 <param name="mass_tolerance" value="0.5"/> 1147 <param name="mass_tolerance" value="0.5"/>
1079 <param name="min_shared" value="2"/> 1148 <param name="min_shared" value="2"/>
1080 </section> 1149 </section>
1097 </conditional> 1166 </conditional>
1098 <param name="in" value="ConsensusID_1_input.idXML"/> 1167 <param name="in" value="ConsensusID_1_input.idXML"/>
1099 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 1168 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1100 <param name="rt_delta" value="0.1"/> 1169 <param name="rt_delta" value="0.1"/>
1101 <param name="mz_delta" value="0.1"/> 1170 <param name="mz_delta" value="0.1"/>
1171 <param name="per_spectrum" value="false"/>
1102 <param name="algorithm" value="PEPMatrix"/> 1172 <param name="algorithm" value="PEPMatrix"/>
1103 <section name="filter"> 1173 <section name="filter">
1104 <param name="considered_hits" value="6"/> 1174 <param name="considered_hits" value="6"/>
1105 <param name="min_support" value="0.0"/> 1175 <param name="min_support" value="0.0"/>
1106 <param name="count_empty" value="false"/> 1176 <param name="count_empty" value="false"/>
1177 <param name="keep_old_scores" value="false"/>
1107 </section> 1178 </section>
1108 <section name="PEPIons"> 1179 <section name="PEPIons">
1109 <param name="mass_tolerance" value="0.5"/> 1180 <param name="mass_tolerance" value="0.5"/>
1110 <param name="min_shared" value="2"/> 1181 <param name="min_shared" value="2"/>
1111 </section> 1182 </section>
1128 </conditional> 1199 </conditional>
1129 <param name="in" value="ConsensusID_1_input.idXML"/> 1200 <param name="in" value="ConsensusID_1_input.idXML"/>
1130 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 1201 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1131 <param name="rt_delta" value="0.1"/> 1202 <param name="rt_delta" value="0.1"/>
1132 <param name="mz_delta" value="0.1"/> 1203 <param name="mz_delta" value="0.1"/>
1204 <param name="per_spectrum" value="false"/>
1133 <param name="algorithm" value="PEPIons"/> 1205 <param name="algorithm" value="PEPIons"/>
1134 <section name="filter"> 1206 <section name="filter">
1135 <param name="considered_hits" value="0"/> 1207 <param name="considered_hits" value="0"/>
1136 <param name="min_support" value="0.0"/> 1208 <param name="min_support" value="0.0"/>
1137 <param name="count_empty" value="false"/> 1209 <param name="count_empty" value="false"/>
1210 <param name="keep_old_scores" value="false"/>
1138 </section> 1211 </section>
1139 <section name="PEPIons"> 1212 <section name="PEPIons">
1140 <param name="mass_tolerance" value="0.5"/> 1213 <param name="mass_tolerance" value="0.5"/>
1141 <param name="min_shared" value="2"/> 1214 <param name="min_shared" value="2"/>
1142 </section> 1215 </section>
1159 </conditional> 1232 </conditional>
1160 <param name="in" value="ConsensusID_1_input.idXML"/> 1233 <param name="in" value="ConsensusID_1_input.idXML"/>
1161 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 1234 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1162 <param name="rt_delta" value="0.1"/> 1235 <param name="rt_delta" value="0.1"/>
1163 <param name="mz_delta" value="0.1"/> 1236 <param name="mz_delta" value="0.1"/>
1237 <param name="per_spectrum" value="false"/>
1164 <param name="algorithm" value="best"/> 1238 <param name="algorithm" value="best"/>
1165 <section name="filter"> 1239 <section name="filter">
1166 <param name="considered_hits" value="0"/> 1240 <param name="considered_hits" value="0"/>
1167 <param name="min_support" value="0.5"/> 1241 <param name="min_support" value="0.5"/>
1168 <param name="count_empty" value="false"/> 1242 <param name="count_empty" value="false"/>
1243 <param name="keep_old_scores" value="false"/>
1244 </section>
1245 <section name="PEPIons">
1246 <param name="mass_tolerance" value="0.5"/>
1247 <param name="min_shared" value="2"/>
1248 </section>
1249 <section name="PEPMatrix">
1250 <param name="matrix" value="identity"/>
1251 <param name="penalty" value="5"/>
1252 </section>
1253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1254 <output name="ctd_out" ftype="xml">
1255 <assert_contents>
1256 <is_valid_xml/>
1257 </assert_contents>
1258 </output>
1259 </test>
1260 <test expect_num_outputs="2">
1261 <conditional name="adv_opts_cond">
1262 <param name="adv_opts_selector" value="advanced"/>
1263 <param name="force" value="false"/>
1264 <param name="test" value="true"/>
1265 </conditional>
1266 <param name="in" value="ConsensusID_6_input.idXML"/>
1267 <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1268 <param name="rt_delta" value="0.1"/>
1269 <param name="mz_delta" value="0.1"/>
1270 <param name="per_spectrum" value="true"/>
1271 <param name="algorithm" value="best"/>
1272 <section name="filter">
1273 <param name="considered_hits" value="0"/>
1274 <param name="min_support" value="0.0"/>
1275 <param name="count_empty" value="false"/>
1276 <param name="keep_old_scores" value="true"/>
1277 </section>
1278 <section name="PEPIons">
1279 <param name="mass_tolerance" value="0.5"/>
1280 <param name="min_shared" value="2"/>
1281 </section>
1282 <section name="PEPMatrix">
1283 <param name="matrix" value="identity"/>
1284 <param name="penalty" value="5"/>
1285 </section>
1286 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1287 <output name="ctd_out" ftype="xml">
1288 <assert_contents>
1289 <is_valid_xml/>
1290 </assert_contents>
1291 </output>
1292 </test>
1293 <test expect_num_outputs="2">
1294 <conditional name="adv_opts_cond">
1295 <param name="adv_opts_selector" value="advanced"/>
1296 <param name="force" value="false"/>
1297 <param name="test" value="true"/>
1298 </conditional>
1299 <param name="in" value="ConsensusID_8_input.idXML"/>
1300 <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1301 <param name="rt_delta" value="0.1"/>
1302 <param name="mz_delta" value="0.1"/>
1303 <param name="per_spectrum" value="true"/>
1304 <param name="algorithm" value="best"/>
1305 <section name="filter">
1306 <param name="considered_hits" value="0"/>
1307 <param name="min_support" value="0.0"/>
1308 <param name="count_empty" value="false"/>
1309 <param name="keep_old_scores" value="true"/>
1169 </section> 1310 </section>
1170 <section name="PEPIons"> 1311 <section name="PEPIons">
1171 <param name="mass_tolerance" value="0.5"/> 1312 <param name="mass_tolerance" value="0.5"/>
1172 <param name="min_shared" value="2"/> 1313 <param name="min_shared" value="2"/>
1173 </section> 1314 </section>
1228 <param name="isotope_error" value=""/> 1369 <param name="isotope_error" value=""/>
1229 <param name="run_percolator" value="false"/> 1370 <param name="run_percolator" value="false"/>
1230 <param name="enzyme" value="trypsin"/> 1371 <param name="enzyme" value="trypsin"/>
1231 <param name="digestion" value="full-digest"/> 1372 <param name="digestion" value="full-digest"/>
1232 <param name="allowed_missed_cleavages" value="0"/> 1373 <param name="allowed_missed_cleavages" value="0"/>
1233 <param name="decoy_format" value="shuffle"/> 1374 <param name="decoy_format" value="peptide-reverse"/>
1234 <param name="keep_terminal_aminos" value="NC"/> 1375 <param name="keep_terminal_aminos" value="NC"/>
1235 <param name="cterm_modifications" value=""/> 1376 <param name="cterm_modifications" value=""/>
1236 <param name="nterm_modifications" value=""/> 1377 <param name="nterm_modifications" value=""/>
1237 <param name="modifications" value=""/> 1378 <param name="modifications" value=""/>
1238 <param name="test_fdr" value="0.01"/> 1379 <param name="test_fdr" value="0.01"/>
1308 <param name="in" value="DatabaseFilter_3.fasta"/> 1449 <param name="in" value="DatabaseFilter_3.fasta"/>
1309 <param name="id" value="DatabaseFilter_3.mzid"/> 1450 <param name="id" value="DatabaseFilter_3.mzid"/>
1310 <param name="method" value="blacklist"/> 1451 <param name="method" value="blacklist"/>
1311 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> 1452 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1312 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1454 <output name="ctd_out" ftype="xml">
1455 <assert_contents>
1456 <is_valid_xml/>
1457 </assert_contents>
1458 </output>
1459 </test>
1460 </xml>
1461 <xml name="autotest_DatabaseSuitability">
1462 <test expect_num_outputs="2">
1463 <conditional name="adv_opts_cond">
1464 <param name="adv_opts_selector" value="advanced"/>
1465 <param name="force" value="false"/>
1466 <param name="test" value="true"/>
1467 </conditional>
1468 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1469 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1470 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1471 <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1472 <section name="algorithm">
1473 <param name="no_rerank" value="false"/>
1474 <param name="reranking_cutoff_percentile" value="0.01"/>
1475 <param name="FDR" value="0.8"/>
1476 </section>
1477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1478 <output name="ctd_out" ftype="xml">
1479 <assert_contents>
1480 <is_valid_xml/>
1481 </assert_contents>
1482 </output>
1483 </test>
1484 <test expect_num_outputs="2">
1485 <conditional name="adv_opts_cond">
1486 <param name="adv_opts_selector" value="advanced"/>
1487 <param name="force" value="false"/>
1488 <param name="test" value="true"/>
1489 </conditional>
1490 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1491 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1492 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1493 <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1494 <section name="algorithm">
1495 <param name="no_rerank" value="false"/>
1496 <param name="reranking_cutoff_percentile" value="0.9"/>
1497 <param name="FDR" value="1.0"/>
1498 </section>
1499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1500 <output name="ctd_out" ftype="xml">
1501 <assert_contents>
1502 <is_valid_xml/>
1503 </assert_contents>
1504 </output>
1505 </test>
1506 <test expect_num_outputs="2">
1507 <conditional name="adv_opts_cond">
1508 <param name="adv_opts_selector" value="advanced"/>
1509 <param name="force" value="false"/>
1510 <param name="test" value="true"/>
1511 </conditional>
1512 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1513 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1514 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1515 <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1516 <section name="algorithm">
1517 <param name="no_rerank" value="true"/>
1518 <param name="reranking_cutoff_percentile" value="0.01"/>
1519 <param name="FDR" value="0.9"/>
1520 </section>
1521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1313 <output name="ctd_out" ftype="xml"> 1522 <output name="ctd_out" ftype="xml">
1314 <assert_contents> 1523 <assert_contents>
1315 <is_valid_xml/> 1524 <is_valid_xml/>
1316 </assert_contents> 1525 </assert_contents>
1317 </output> 1526 </output>
1473 </output> 1682 </output>
1474 </test> 1683 </test>
1475 </xml> 1684 </xml>
1476 <xml name="autotest_DeMeanderize"> 1685 <xml name="autotest_DeMeanderize">
1477 </xml> 1686 </xml>
1687 <xml name="autotest_DigestorMotif">
1688 </xml>
1478 <xml name="autotest_Digestor"> 1689 <xml name="autotest_Digestor">
1479 </xml> 1690 </xml>
1480 <xml name="autotest_DTAExtractor"> 1691 <xml name="autotest_DTAExtractor">
1481 <test expect_num_outputs="1"> 1692 <test expect_num_outputs="1">
1482 <conditional name="adv_opts_cond"> 1693 <conditional name="adv_opts_cond">
1544 <param name="force" value="false"/> 1755 <param name="force" value="false"/>
1545 <param name="test" value="true"/> 1756 <param name="test" value="true"/>
1546 </conditional> 1757 </conditional>
1547 <param name="in" value="FidoAdapter_1_input.idXML"/> 1758 <param name="in" value="FidoAdapter_1_input.idXML"/>
1548 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 1759 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1760 <param name="out_type" value="idxml"/>
1549 <param name="protein_fdr" value="false"/> 1761 <param name="protein_fdr" value="false"/>
1550 <param name="greedy_group_resolution" value="none"/> 1762 <param name="greedy_group_resolution" value="none"/>
1551 <param name="max_psms_extreme_probability" value="1.0"/> 1763 <param name="max_psms_extreme_probability" value="1.0"/>
1552 <section name="algorithm"> 1764 <section name="algorithm">
1553 <param name="psm_probability_cutoff" value="0.001"/> 1765 <param name="psm_probability_cutoff" value="0.001"/>
1554 <param name="top_PSMs" value="1"/> 1766 <param name="top_PSMs" value="1"/>
1767 <param name="keep_best_PSM_only" value="true"/>
1555 <param name="update_PSM_probabilities" value="true"/> 1768 <param name="update_PSM_probabilities" value="true"/>
1556 <param name="user_defined_priors" value="false"/> 1769 <param name="user_defined_priors" value="false"/>
1557 <param name="annotate_group_probabilities" value="true"/> 1770 <param name="annotate_group_probabilities" value="true"/>
1558 <param name="use_ids_outside_features" value="false"/> 1771 <param name="use_ids_outside_features" value="false"/>
1559 <section name="model_parameters"> 1772 <section name="model_parameters">
1572 <param name="p_norm_inference" value="1.0"/> 1785 <param name="p_norm_inference" value="1.0"/>
1573 </section> 1786 </section>
1574 <section name="param_optimize"> 1787 <section name="param_optimize">
1575 <param name="aucweight" value="0.3"/> 1788 <param name="aucweight" value="0.3"/>
1576 <param name="conservative_fdr" value="true"/> 1789 <param name="conservative_fdr" value="true"/>
1790 <param name="regularized_fdr" value="true"/>
1791 </section>
1792 </section>
1793 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1794 <output name="ctd_out" ftype="xml">
1795 <assert_contents>
1796 <is_valid_xml/>
1797 </assert_contents>
1798 </output>
1799 </test>
1800 <test expect_num_outputs="2">
1801 <conditional name="adv_opts_cond">
1802 <param name="adv_opts_selector" value="advanced"/>
1803 <param name="conservative_fdr" value="true"/>
1804 <param name="min_psms_extreme_probability" value="0.0"/>
1805 <param name="force" value="false"/>
1806 <param name="test" value="true"/>
1807 </conditional>
1808 <param name="in" value="Epifany_2_input.consensusXML"/>
1809 <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1810 <param name="out_type" value="consensusXML"/>
1811 <param name="protein_fdr" value="false"/>
1812 <param name="greedy_group_resolution" value="none"/>
1813 <param name="max_psms_extreme_probability" value="1.0"/>
1814 <section name="algorithm">
1815 <param name="psm_probability_cutoff" value="0.001"/>
1816 <param name="top_PSMs" value="1"/>
1817 <param name="keep_best_PSM_only" value="true"/>
1818 <param name="update_PSM_probabilities" value="true"/>
1819 <param name="user_defined_priors" value="false"/>
1820 <param name="annotate_group_probabilities" value="true"/>
1821 <param name="use_ids_outside_features" value="false"/>
1822 <section name="model_parameters">
1823 <param name="prot_prior" value="0.7"/>
1824 <param name="pep_emission" value="0.1"/>
1825 <param name="pep_spurious_emission" value="0.001"/>
1826 <param name="pep_prior" value="0.1"/>
1827 <param name="regularize" value="false"/>
1828 <param name="extended_model" value="false"/>
1829 </section>
1830 <section name="loopy_belief_propagation">
1831 <param name="scheduling_type" value="priority"/>
1832 <param name="convergence_threshold" value="1e-05"/>
1833 <param name="dampening_lambda" value="0.001"/>
1834 <param name="max_nr_iterations" value="2147483647"/>
1835 <param name="p_norm_inference" value="1.0"/>
1836 </section>
1837 <section name="param_optimize">
1838 <param name="aucweight" value="0.3"/>
1839 <param name="conservative_fdr" value="true"/>
1840 <param name="regularized_fdr" value="true"/>
1841 </section>
1842 </section>
1843 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1844 <output name="ctd_out" ftype="xml">
1845 <assert_contents>
1846 <is_valid_xml/>
1847 </assert_contents>
1848 </output>
1849 </test>
1850 <test expect_num_outputs="2">
1851 <conditional name="adv_opts_cond">
1852 <param name="adv_opts_selector" value="advanced"/>
1853 <param name="conservative_fdr" value="true"/>
1854 <param name="min_psms_extreme_probability" value="0.0"/>
1855 <param name="force" value="false"/>
1856 <param name="test" value="true"/>
1857 </conditional>
1858 <param name="in" value="Epifany_2_input.consensusXML"/>
1859 <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1860 <param name="out_type" value="consensusXML"/>
1861 <param name="protein_fdr" value="false"/>
1862 <param name="greedy_group_resolution" value="none"/>
1863 <param name="max_psms_extreme_probability" value="1.0"/>
1864 <section name="algorithm">
1865 <param name="psm_probability_cutoff" value="0.001"/>
1866 <param name="top_PSMs" value="1"/>
1867 <param name="keep_best_PSM_only" value="false"/>
1868 <param name="update_PSM_probabilities" value="true"/>
1869 <param name="user_defined_priors" value="false"/>
1870 <param name="annotate_group_probabilities" value="true"/>
1871 <param name="use_ids_outside_features" value="false"/>
1872 <section name="model_parameters">
1873 <param name="prot_prior" value="0.7"/>
1874 <param name="pep_emission" value="0.1"/>
1875 <param name="pep_spurious_emission" value="0.001"/>
1876 <param name="pep_prior" value="0.1"/>
1877 <param name="regularize" value="false"/>
1878 <param name="extended_model" value="false"/>
1879 </section>
1880 <section name="loopy_belief_propagation">
1881 <param name="scheduling_type" value="priority"/>
1882 <param name="convergence_threshold" value="1e-05"/>
1883 <param name="dampening_lambda" value="0.001"/>
1884 <param name="max_nr_iterations" value="2147483647"/>
1885 <param name="p_norm_inference" value="1.0"/>
1886 </section>
1887 <section name="param_optimize">
1888 <param name="aucweight" value="0.3"/>
1889 <param name="conservative_fdr" value="true"/>
1890 <param name="regularized_fdr" value="true"/>
1577 </section> 1891 </section>
1578 </section> 1892 </section>
1579 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 1893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1580 <output name="ctd_out" ftype="xml"> 1894 <output name="ctd_out" ftype="xml">
1581 <assert_contents> 1895 <assert_contents>
1974 <section name="model"> 2288 <section name="model">
1975 <param name="type" value="none"/> 2289 <param name="type" value="none"/>
1976 <param name="add_zeros" value="0.2"/> 2290 <param name="add_zeros" value="0.2"/>
1977 <param name="unweighted_fit" value="false"/> 2291 <param name="unweighted_fit" value="false"/>
1978 <param name="no_imputation" value="false"/> 2292 <param name="no_imputation" value="false"/>
2293 <param name="each_trace" value="false"/>
1979 <section name="check"> 2294 <section name="check">
1980 <param name="min_area" value="1.0"/> 2295 <param name="min_area" value="1.0"/>
1981 <param name="boundaries" value="0.5"/> 2296 <param name="boundaries" value="0.5"/>
1982 <param name="width" value="10.0"/> 2297 <param name="width" value="10.0"/>
1983 <param name="asymmetry" value="10.0"/> 2298 <param name="asymmetry" value="10.0"/>
2029 <section name="model"> 2344 <section name="model">
2030 <param name="type" value="symmetric"/> 2345 <param name="type" value="symmetric"/>
2031 <param name="add_zeros" value="0.2"/> 2346 <param name="add_zeros" value="0.2"/>
2032 <param name="unweighted_fit" value="false"/> 2347 <param name="unweighted_fit" value="false"/>
2033 <param name="no_imputation" value="false"/> 2348 <param name="no_imputation" value="false"/>
2034 <section name="check"> 2349 <param name="each_trace" value="false"/>
2035 <param name="min_area" value="1.0"/>
2036 <param name="boundaries" value="0.5"/>
2037 <param name="width" value="10.0"/>
2038 <param name="asymmetry" value="10.0"/>
2039 </section>
2040 </section>
2041 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2042 <output name="ctd_out" ftype="xml">
2043 <assert_contents>
2044 <is_valid_xml/>
2045 </assert_contents>
2046 </output>
2047 </test>
2048 <test expect_num_outputs="2">
2049 <conditional name="adv_opts_cond">
2050 <param name="adv_opts_selector" value="advanced"/>
2051 <param name="force" value="false"/>
2052 <param name="test" value="true"/>
2053 </conditional>
2054 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2055 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2056 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2057 <section name="extract">
2058 <param name="batch_size" value="10"/>
2059 <param name="mz_window" value="0.1"/>
2060 <param name="n_isotopes" value="2"/>
2061 <param name="isotope_pmin" value="0.0"/>
2062 <param name="rt_quantile" value="0.95"/>
2063 <param name="rt_window" value="0.0"/>
2064 </section>
2065 <section name="detect">
2066 <param name="peak_width" value="60.0"/>
2067 <param name="min_peak_width" value="0.2"/>
2068 <param name="signal_to_noise" value="0.8"/>
2069 <param name="mapping_tolerance" value="0.0"/>
2070 </section>
2071 <section name="svm">
2072 <param name="samples" value="0"/>
2073 <param name="no_selection" value="false"/>
2074 <param name="kernel" value="RBF"/>
2075 <param name="xval" value="5"/>
2076 <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"/>
2077 <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"/>
2078 <param name="epsilon" value="0.001"/>
2079 <param name="cache_size" value="100.0"/>
2080 <param name="no_shrinking" value="false"/>
2081 <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"/>
2082 <param name="min_prob" value="0.0"/>
2083 </section>
2084 <section name="model">
2085 <param name="type" value="none"/>
2086 <param name="add_zeros" value="0.2"/>
2087 <param name="unweighted_fit" value="false"/>
2088 <param name="no_imputation" value="false"/>
2089 <section name="check"> 2350 <section name="check">
2090 <param name="min_area" value="1.0"/> 2351 <param name="min_area" value="1.0"/>
2091 <param name="boundaries" value="0.5"/> 2352 <param name="boundaries" value="0.5"/>
2092 <param name="width" value="10.0"/> 2353 <param name="width" value="10.0"/>
2093 <param name="asymmetry" value="10.0"/> 2354 <param name="asymmetry" value="10.0"/>
2127 <section name="model"> 2388 <section name="model">
2128 <param name="type" value="symmetric"/> 2389 <param name="type" value="symmetric"/>
2129 <param name="add_zeros" value="0.2"/> 2390 <param name="add_zeros" value="0.2"/>
2130 <param name="unweighted_fit" value="false"/> 2391 <param name="unweighted_fit" value="false"/>
2131 <param name="no_imputation" value="false"/> 2392 <param name="no_imputation" value="false"/>
2393 <param name="each_trace" value="false"/>
2132 <section name="check"> 2394 <section name="check">
2133 <param name="min_area" value="1.0"/> 2395 <param name="min_area" value="1.0"/>
2134 <param name="boundaries" value="0.5"/> 2396 <param name="boundaries" value="0.5"/>
2135 <param name="width" value="10.0"/> 2397 <param name="width" value="10.0"/>
2136 <param name="asymmetry" value="10.0"/> 2398 <param name="asymmetry" value="10.0"/>
4072 <param name="log2_states_precalc" value="0"/> 4334 <param name="log2_states_precalc" value="0"/>
4073 <param name="force" value="false"/> 4335 <param name="force" value="false"/>
4074 <param name="test" value="true"/> 4336 <param name="test" value="true"/>
4075 </conditional> 4337 </conditional>
4076 <param name="in" value="FidoAdapter_1_input.idXML"/> 4338 <param name="in" value="FidoAdapter_1_input.idXML"/>
4077 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 4339 <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4078 <param name="separate_runs" value="false"/> 4340 <param name="separate_runs" value="false"/>
4079 <param name="greedy_group_resolution" value="false"/> 4341 <param name="greedy_group_resolution" value="false"/>
4080 <param name="no_cleanup" value="false"/> 4342 <param name="no_cleanup" value="false"/>
4081 <param name="all_PSMs" value="false"/> 4343 <param name="all_PSMs" value="false"/>
4082 <param name="group_level" value="false"/> 4344 <param name="group_level" value="false"/>
4981 <param name="force" value="false"/> 5243 <param name="force" value="false"/>
4982 <param name="test" value="true"/> 5244 <param name="test" value="true"/>
4983 </conditional> 5245 </conditional>
4984 <param name="in" value="FileConverter_30_output.mzML"/> 5246 <param name="in" value="FileConverter_30_output.mzML"/>
4985 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 5247 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5248 <param name="out_type" value="mzML"/>
5249 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5250 <output name="ctd_out" ftype="xml">
5251 <assert_contents>
5252 <is_valid_xml/>
5253 </assert_contents>
5254 </output>
5255 </test>
5256 <test expect_num_outputs="2">
5257 <conditional name="adv_opts_cond">
5258 <param name="adv_opts_selector" value="advanced"/>
5259 <param name="UID_postprocessing" value="ensure"/>
5260 <param name="TIC_DTA2D" value="false"/>
5261 <param name="MGF_compact" value="false"/>
5262 <param name="force_MaxQuant_compatibility" value="false"/>
5263 <param name="convert_to_chromatograms" value="false"/>
5264 <param name="force_TPP_compatibility" value="false"/>
5265 <param name="change_im_format" value="none"/>
5266 <param name="write_scan_index" value="true"/>
5267 <param name="lossy_compression" value="false"/>
5268 <param name="lossy_mass_accuracy" value="-1.0"/>
5269 <param name="process_lowmemory" value="false"/>
5270 <param name="no_peak_picking" value="false"/>
5271 <param name="force" value="false"/>
5272 <param name="test" value="true"/>
5273 </conditional>
5274 <param name="in" value="FileConverter_32_input.mzML"/>
5275 <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4986 <param name="out_type" value="mzML"/> 5276 <param name="out_type" value="mzML"/>
4987 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 5277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4988 <output name="ctd_out" ftype="xml"> 5278 <output name="ctd_out" ftype="xml">
4989 <assert_contents> 5279 <assert_contents>
4990 <is_valid_xml/> 5280 <is_valid_xml/>
11127 <param name="ignore_proteins_per_peptide" value="false"/> 11417 <param name="ignore_proteins_per_peptide" value="false"/>
11128 <param name="scan_regex" value=""/> 11418 <param name="scan_regex" value=""/>
11129 <param name="no_spectra_data_override" value="false"/> 11419 <param name="no_spectra_data_override" value="false"/>
11130 <param name="no_spectra_references_override" value="false"/> 11420 <param name="no_spectra_references_override" value="false"/>
11131 <param name="add_ionmatch_annotation" value="0.0"/> 11421 <param name="add_ionmatch_annotation" value="0.0"/>
11422 <param name="concatenate_peptides" value="false"/>
11423 <param name="number_of_hits" value="1"/>
11132 <param name="force" value="false"/> 11424 <param name="force" value="false"/>
11133 <param name="test" value="true"/> 11425 <param name="test" value="true"/>
11134 </conditional> 11426 </conditional>
11135 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> 11427 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11136 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11428 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11152 <param name="ignore_proteins_per_peptide" value="false"/> 11444 <param name="ignore_proteins_per_peptide" value="false"/>
11153 <param name="scan_regex" value=""/> 11445 <param name="scan_regex" value=""/>
11154 <param name="no_spectra_data_override" value="false"/> 11446 <param name="no_spectra_data_override" value="false"/>
11155 <param name="no_spectra_references_override" value="false"/> 11447 <param name="no_spectra_references_override" value="false"/>
11156 <param name="add_ionmatch_annotation" value="0.0"/> 11448 <param name="add_ionmatch_annotation" value="0.0"/>
11449 <param name="concatenate_peptides" value="false"/>
11450 <param name="number_of_hits" value="1"/>
11157 <param name="force" value="false"/> 11451 <param name="force" value="false"/>
11158 <param name="test" value="true"/> 11452 <param name="test" value="true"/>
11159 </conditional> 11453 </conditional>
11160 <param name="in" value="PepXMLFile_test.pepxml"/> 11454 <param name="in" value="PepXMLFile_test.pepxml"/>
11161 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11455 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11177 <param name="ignore_proteins_per_peptide" value="false"/> 11471 <param name="ignore_proteins_per_peptide" value="false"/>
11178 <param name="scan_regex" value=""/> 11472 <param name="scan_regex" value=""/>
11179 <param name="no_spectra_data_override" value="false"/> 11473 <param name="no_spectra_data_override" value="false"/>
11180 <param name="no_spectra_references_override" value="false"/> 11474 <param name="no_spectra_references_override" value="false"/>
11181 <param name="add_ionmatch_annotation" value="0.0"/> 11475 <param name="add_ionmatch_annotation" value="0.0"/>
11476 <param name="concatenate_peptides" value="false"/>
11477 <param name="number_of_hits" value="1"/>
11182 <param name="force" value="false"/> 11478 <param name="force" value="false"/>
11183 <param name="test" value="true"/> 11479 <param name="test" value="true"/>
11184 </conditional> 11480 </conditional>
11185 <param name="in" value="IDFileConverter_3_input.protXML"/> 11481 <param name="in" value="IDFileConverter_3_input.protXML"/>
11186 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11482 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11201 <param name="ignore_proteins_per_peptide" value="false"/> 11497 <param name="ignore_proteins_per_peptide" value="false"/>
11202 <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/> 11498 <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
11203 <param name="no_spectra_data_override" value="false"/> 11499 <param name="no_spectra_data_override" value="false"/>
11204 <param name="no_spectra_references_override" value="false"/> 11500 <param name="no_spectra_references_override" value="false"/>
11205 <param name="add_ionmatch_annotation" value="0.0"/> 11501 <param name="add_ionmatch_annotation" value="0.0"/>
11502 <param name="concatenate_peptides" value="false"/>
11503 <param name="number_of_hits" value="1"/>
11206 <param name="force" value="false"/> 11504 <param name="force" value="false"/>
11207 <param name="test" value="true"/> 11505 <param name="test" value="true"/>
11208 </conditional> 11506 </conditional>
11209 <param name="in" value="IDFileConverter_1_input1.mascotXML"/> 11507 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11210 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11508 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11226 <param name="ignore_proteins_per_peptide" value="false"/> 11524 <param name="ignore_proteins_per_peptide" value="false"/>
11227 <param name="scan_regex" value=""/> 11525 <param name="scan_regex" value=""/>
11228 <param name="no_spectra_data_override" value="false"/> 11526 <param name="no_spectra_data_override" value="false"/>
11229 <param name="no_spectra_references_override" value="false"/> 11527 <param name="no_spectra_references_override" value="false"/>
11230 <param name="add_ionmatch_annotation" value="0.0"/> 11528 <param name="add_ionmatch_annotation" value="0.0"/>
11529 <param name="concatenate_peptides" value="false"/>
11530 <param name="number_of_hits" value="1"/>
11231 <param name="force" value="false"/> 11531 <param name="force" value="false"/>
11232 <param name="test" value="true"/> 11532 <param name="test" value="true"/>
11233 </conditional> 11533 </conditional>
11234 <param name="in" value="IDFileConverter_6_input1.pepXML"/> 11534 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
11235 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11535 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11251 <param name="ignore_proteins_per_peptide" value="false"/> 11551 <param name="ignore_proteins_per_peptide" value="false"/>
11252 <param name="scan_regex" value=""/> 11552 <param name="scan_regex" value=""/>
11253 <param name="no_spectra_data_override" value="false"/> 11553 <param name="no_spectra_data_override" value="false"/>
11254 <param name="no_spectra_references_override" value="false"/> 11554 <param name="no_spectra_references_override" value="false"/>
11255 <param name="add_ionmatch_annotation" value="0.0"/> 11555 <param name="add_ionmatch_annotation" value="0.0"/>
11556 <param name="concatenate_peptides" value="false"/>
11557 <param name="number_of_hits" value="1"/>
11256 <param name="force" value="false"/> 11558 <param name="force" value="false"/>
11257 <param name="test" value="true"/> 11559 <param name="test" value="true"/>
11258 </conditional> 11560 </conditional>
11259 <param name="in" value="IDFileConverter_7_input1.xml"/> 11561 <param name="in" value="IDFileConverter_7_input1.xml"/>
11260 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11562 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11275 <param name="ignore_proteins_per_peptide" value="false"/> 11577 <param name="ignore_proteins_per_peptide" value="false"/>
11276 <param name="scan_regex" value=""/> 11578 <param name="scan_regex" value=""/>
11277 <param name="no_spectra_data_override" value="false"/> 11579 <param name="no_spectra_data_override" value="false"/>
11278 <param name="no_spectra_references_override" value="false"/> 11580 <param name="no_spectra_references_override" value="false"/>
11279 <param name="add_ionmatch_annotation" value="0.0"/> 11581 <param name="add_ionmatch_annotation" value="0.0"/>
11582 <param name="concatenate_peptides" value="false"/>
11583 <param name="number_of_hits" value="1"/>
11280 <param name="force" value="false"/> 11584 <param name="force" value="false"/>
11281 <param name="test" value="true"/> 11585 <param name="test" value="true"/>
11282 </conditional> 11586 </conditional>
11283 <param name="in" value="IDFileConverter_8_input.mzid"/> 11587 <param name="in" value="IDFileConverter_8_input.mzid"/>
11284 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11588 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11299 <param name="ignore_proteins_per_peptide" value="false"/> 11603 <param name="ignore_proteins_per_peptide" value="false"/>
11300 <param name="scan_regex" value=""/> 11604 <param name="scan_regex" value=""/>
11301 <param name="no_spectra_data_override" value="false"/> 11605 <param name="no_spectra_data_override" value="false"/>
11302 <param name="no_spectra_references_override" value="false"/> 11606 <param name="no_spectra_references_override" value="false"/>
11303 <param name="add_ionmatch_annotation" value="0.0"/> 11607 <param name="add_ionmatch_annotation" value="0.0"/>
11608 <param name="concatenate_peptides" value="false"/>
11609 <param name="number_of_hits" value="1"/>
11304 <param name="force" value="false"/> 11610 <param name="force" value="false"/>
11305 <param name="test" value="true"/> 11611 <param name="test" value="true"/>
11306 </conditional> 11612 </conditional>
11307 <param name="in" value="IDFileConverter_9_input.idXML"/> 11613 <param name="in" value="IDFileConverter_9_input.idXML"/>
11308 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> 11614 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
11323 <param name="ignore_proteins_per_peptide" value="false"/> 11629 <param name="ignore_proteins_per_peptide" value="false"/>
11324 <param name="scan_regex" value=""/> 11630 <param name="scan_regex" value=""/>
11325 <param name="no_spectra_data_override" value="false"/> 11631 <param name="no_spectra_data_override" value="false"/>
11326 <param name="no_spectra_references_override" value="false"/> 11632 <param name="no_spectra_references_override" value="false"/>
11327 <param name="add_ionmatch_annotation" value="0.0"/> 11633 <param name="add_ionmatch_annotation" value="0.0"/>
11634 <param name="concatenate_peptides" value="false"/>
11635 <param name="number_of_hits" value="1"/>
11328 <param name="force" value="false"/> 11636 <param name="force" value="false"/>
11329 <param name="test" value="true"/> 11637 <param name="test" value="true"/>
11330 </conditional> 11638 </conditional>
11331 <param name="in" value="IDFileConverter_10_input.pepXML"/> 11639 <param name="in" value="IDFileConverter_10_input.pepXML"/>
11332 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11640 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11347 <param name="ignore_proteins_per_peptide" value="false"/> 11655 <param name="ignore_proteins_per_peptide" value="false"/>
11348 <param name="scan_regex" value=""/> 11656 <param name="scan_regex" value=""/>
11349 <param name="no_spectra_data_override" value="false"/> 11657 <param name="no_spectra_data_override" value="false"/>
11350 <param name="no_spectra_references_override" value="false"/> 11658 <param name="no_spectra_references_override" value="false"/>
11351 <param name="add_ionmatch_annotation" value="0.0"/> 11659 <param name="add_ionmatch_annotation" value="0.0"/>
11660 <param name="concatenate_peptides" value="false"/>
11661 <param name="number_of_hits" value="1"/>
11352 <param name="force" value="false"/> 11662 <param name="force" value="false"/>
11353 <param name="test" value="true"/> 11663 <param name="test" value="true"/>
11354 </conditional> 11664 </conditional>
11355 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> 11665 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
11356 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11666 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11371 <param name="ignore_proteins_per_peptide" value="false"/> 11681 <param name="ignore_proteins_per_peptide" value="false"/>
11372 <param name="scan_regex" value=""/> 11682 <param name="scan_regex" value=""/>
11373 <param name="no_spectra_data_override" value="false"/> 11683 <param name="no_spectra_data_override" value="false"/>
11374 <param name="no_spectra_references_override" value="false"/> 11684 <param name="no_spectra_references_override" value="false"/>
11375 <param name="add_ionmatch_annotation" value="0.0"/> 11685 <param name="add_ionmatch_annotation" value="0.0"/>
11686 <param name="concatenate_peptides" value="false"/>
11687 <param name="number_of_hits" value="1"/>
11376 <param name="force" value="false"/> 11688 <param name="force" value="false"/>
11377 <param name="test" value="true"/> 11689 <param name="test" value="true"/>
11378 </conditional> 11690 </conditional>
11379 <param name="in" value="IDFileConverter_12_input.psms"/> 11691 <param name="in" value="IDFileConverter_12_input.psms"/>
11380 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11692 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11395 <param name="ignore_proteins_per_peptide" value="false"/> 11707 <param name="ignore_proteins_per_peptide" value="false"/>
11396 <param name="scan_regex" value=""/> 11708 <param name="scan_regex" value=""/>
11397 <param name="no_spectra_data_override" value="false"/> 11709 <param name="no_spectra_data_override" value="false"/>
11398 <param name="no_spectra_references_override" value="false"/> 11710 <param name="no_spectra_references_override" value="false"/>
11399 <param name="add_ionmatch_annotation" value="0.0"/> 11711 <param name="add_ionmatch_annotation" value="0.0"/>
11712 <param name="concatenate_peptides" value="false"/>
11713 <param name="number_of_hits" value="1"/>
11400 <param name="force" value="false"/> 11714 <param name="force" value="false"/>
11401 <param name="test" value="true"/> 11715 <param name="test" value="true"/>
11402 </conditional> 11716 </conditional>
11403 <param name="in" value="IDFileConverter_12_input.psms"/> 11717 <param name="in" value="IDFileConverter_12_input.psms"/>
11404 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11718 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11419 <param name="ignore_proteins_per_peptide" value="false"/> 11733 <param name="ignore_proteins_per_peptide" value="false"/>
11420 <param name="scan_regex" value=""/> 11734 <param name="scan_regex" value=""/>
11421 <param name="no_spectra_data_override" value="false"/> 11735 <param name="no_spectra_data_override" value="false"/>
11422 <param name="no_spectra_references_override" value="false"/> 11736 <param name="no_spectra_references_override" value="false"/>
11423 <param name="add_ionmatch_annotation" value="0.0"/> 11737 <param name="add_ionmatch_annotation" value="0.0"/>
11738 <param name="concatenate_peptides" value="false"/>
11739 <param name="number_of_hits" value="1"/>
11424 <param name="force" value="false"/> 11740 <param name="force" value="false"/>
11425 <param name="test" value="true"/> 11741 <param name="test" value="true"/>
11426 </conditional> 11742 </conditional>
11427 <param name="in" value="IDFileConverter_12_input.psms"/> 11743 <param name="in" value="IDFileConverter_12_input.psms"/>
11428 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11744 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11443 <param name="ignore_proteins_per_peptide" value="false"/> 11759 <param name="ignore_proteins_per_peptide" value="false"/>
11444 <param name="scan_regex" value=""/> 11760 <param name="scan_regex" value=""/>
11445 <param name="no_spectra_data_override" value="false"/> 11761 <param name="no_spectra_data_override" value="false"/>
11446 <param name="no_spectra_references_override" value="false"/> 11762 <param name="no_spectra_references_override" value="false"/>
11447 <param name="add_ionmatch_annotation" value="0.0"/> 11763 <param name="add_ionmatch_annotation" value="0.0"/>
11764 <param name="concatenate_peptides" value="false"/>
11765 <param name="number_of_hits" value="1"/>
11448 <param name="force" value="false"/> 11766 <param name="force" value="false"/>
11449 <param name="test" value="true"/> 11767 <param name="test" value="true"/>
11450 </conditional> 11768 </conditional>
11451 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> 11769 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11452 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11770 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11468 <param name="ignore_proteins_per_peptide" value="false"/> 11786 <param name="ignore_proteins_per_peptide" value="false"/>
11469 <param name="scan_regex" value=""/> 11787 <param name="scan_regex" value=""/>
11470 <param name="no_spectra_data_override" value="false"/> 11788 <param name="no_spectra_data_override" value="false"/>
11471 <param name="no_spectra_references_override" value="false"/> 11789 <param name="no_spectra_references_override" value="false"/>
11472 <param name="add_ionmatch_annotation" value="0.0"/> 11790 <param name="add_ionmatch_annotation" value="0.0"/>
11791 <param name="concatenate_peptides" value="false"/>
11792 <param name="number_of_hits" value="1"/>
11473 <param name="force" value="false"/> 11793 <param name="force" value="false"/>
11474 <param name="test" value="true"/> 11794 <param name="test" value="true"/>
11475 </conditional> 11795 </conditional>
11476 <param name="in" value="IDFileConverter_16_input.pepXML"/> 11796 <param name="in" value="IDFileConverter_16_input.pepXML"/>
11477 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11797 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11492 <param name="ignore_proteins_per_peptide" value="false"/> 11812 <param name="ignore_proteins_per_peptide" value="false"/>
11493 <param name="scan_regex" value=""/> 11813 <param name="scan_regex" value=""/>
11494 <param name="no_spectra_data_override" value="false"/> 11814 <param name="no_spectra_data_override" value="false"/>
11495 <param name="no_spectra_references_override" value="false"/> 11815 <param name="no_spectra_references_override" value="false"/>
11496 <param name="add_ionmatch_annotation" value="0.0"/> 11816 <param name="add_ionmatch_annotation" value="0.0"/>
11817 <param name="concatenate_peptides" value="false"/>
11818 <param name="number_of_hits" value="1"/>
11497 <param name="force" value="false"/> 11819 <param name="force" value="false"/>
11498 <param name="test" value="true"/> 11820 <param name="test" value="true"/>
11499 </conditional> 11821 </conditional>
11500 <param name="in" value="IDFileConverter_17_input.idXML"/> 11822 <param name="in" value="IDFileConverter_17_input.idXML"/>
11501 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> 11823 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11516 <param name="ignore_proteins_per_peptide" value="false"/> 11838 <param name="ignore_proteins_per_peptide" value="false"/>
11517 <param name="scan_regex" value=""/> 11839 <param name="scan_regex" value=""/>
11518 <param name="no_spectra_data_override" value="false"/> 11840 <param name="no_spectra_data_override" value="false"/>
11519 <param name="no_spectra_references_override" value="false"/> 11841 <param name="no_spectra_references_override" value="false"/>
11520 <param name="add_ionmatch_annotation" value="0.0"/> 11842 <param name="add_ionmatch_annotation" value="0.0"/>
11843 <param name="concatenate_peptides" value="false"/>
11844 <param name="number_of_hits" value="1"/>
11521 <param name="force" value="false"/> 11845 <param name="force" value="false"/>
11522 <param name="test" value="true"/> 11846 <param name="test" value="true"/>
11523 </conditional> 11847 </conditional>
11524 <param name="in" value="IDFileConverter_18_input.idXML"/> 11848 <param name="in" value="IDFileConverter_18_input.idXML"/>
11525 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> 11849 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11540 <param name="ignore_proteins_per_peptide" value="false"/> 11864 <param name="ignore_proteins_per_peptide" value="false"/>
11541 <param name="scan_regex" value=""/> 11865 <param name="scan_regex" value=""/>
11542 <param name="no_spectra_data_override" value="false"/> 11866 <param name="no_spectra_data_override" value="false"/>
11543 <param name="no_spectra_references_override" value="false"/> 11867 <param name="no_spectra_references_override" value="false"/>
11544 <param name="add_ionmatch_annotation" value="0.0"/> 11868 <param name="add_ionmatch_annotation" value="0.0"/>
11869 <param name="concatenate_peptides" value="false"/>
11870 <param name="number_of_hits" value="1"/>
11545 <param name="force" value="false"/> 11871 <param name="force" value="false"/>
11546 <param name="test" value="true"/> 11872 <param name="test" value="true"/>
11547 </conditional> 11873 </conditional>
11548 <param name="in" value="IDFileConverter_19_input.idXML"/> 11874 <param name="in" value="IDFileConverter_19_input.idXML"/>
11549 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> 11875 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11564 <param name="ignore_proteins_per_peptide" value="false"/> 11890 <param name="ignore_proteins_per_peptide" value="false"/>
11565 <param name="scan_regex" value=""/> 11891 <param name="scan_regex" value=""/>
11566 <param name="no_spectra_data_override" value="false"/> 11892 <param name="no_spectra_data_override" value="false"/>
11567 <param name="no_spectra_references_override" value="false"/> 11893 <param name="no_spectra_references_override" value="false"/>
11568 <param name="add_ionmatch_annotation" value="0.0"/> 11894 <param name="add_ionmatch_annotation" value="0.0"/>
11895 <param name="concatenate_peptides" value="false"/>
11896 <param name="number_of_hits" value="1"/>
11569 <param name="force" value="false"/> 11897 <param name="force" value="false"/>
11570 <param name="test" value="true"/> 11898 <param name="test" value="true"/>
11571 </conditional> 11899 </conditional>
11572 <param name="in" value="IDFileConverter_20_input.idXML"/> 11900 <param name="in" value="IDFileConverter_20_input.idXML"/>
11573 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> 11901 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11588 <param name="ignore_proteins_per_peptide" value="false"/> 11916 <param name="ignore_proteins_per_peptide" value="false"/>
11589 <param name="scan_regex" value=""/> 11917 <param name="scan_regex" value=""/>
11590 <param name="no_spectra_data_override" value="false"/> 11918 <param name="no_spectra_data_override" value="false"/>
11591 <param name="no_spectra_references_override" value="false"/> 11919 <param name="no_spectra_references_override" value="false"/>
11592 <param name="add_ionmatch_annotation" value="0.0"/> 11920 <param name="add_ionmatch_annotation" value="0.0"/>
11921 <param name="concatenate_peptides" value="false"/>
11922 <param name="number_of_hits" value="1"/>
11593 <param name="force" value="false"/> 11923 <param name="force" value="false"/>
11594 <param name="test" value="true"/> 11924 <param name="test" value="true"/>
11595 </conditional> 11925 </conditional>
11596 <param name="in" value="IDFileConverter_21_input.idXML"/> 11926 <param name="in" value="IDFileConverter_21_input.idXML"/>
11597 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11927 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11613 <param name="ignore_proteins_per_peptide" value="false"/> 11943 <param name="ignore_proteins_per_peptide" value="false"/>
11614 <param name="scan_regex" value=""/> 11944 <param name="scan_regex" value=""/>
11615 <param name="no_spectra_data_override" value="false"/> 11945 <param name="no_spectra_data_override" value="false"/>
11616 <param name="no_spectra_references_override" value="false"/> 11946 <param name="no_spectra_references_override" value="false"/>
11617 <param name="add_ionmatch_annotation" value="0.01"/> 11947 <param name="add_ionmatch_annotation" value="0.01"/>
11948 <param name="concatenate_peptides" value="false"/>
11949 <param name="number_of_hits" value="1"/>
11618 <param name="force" value="false"/> 11950 <param name="force" value="false"/>
11619 <param name="test" value="true"/> 11951 <param name="test" value="true"/>
11620 </conditional> 11952 </conditional>
11621 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> 11953 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11622 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11954 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11638 <param name="ignore_proteins_per_peptide" value="false"/> 11970 <param name="ignore_proteins_per_peptide" value="false"/>
11639 <param name="scan_regex" value=""/> 11971 <param name="scan_regex" value=""/>
11640 <param name="no_spectra_data_override" value="false"/> 11972 <param name="no_spectra_data_override" value="false"/>
11641 <param name="no_spectra_references_override" value="false"/> 11973 <param name="no_spectra_references_override" value="false"/>
11642 <param name="add_ionmatch_annotation" value="0.0"/> 11974 <param name="add_ionmatch_annotation" value="0.0"/>
11975 <param name="concatenate_peptides" value="false"/>
11976 <param name="number_of_hits" value="1"/>
11643 <param name="force" value="false"/> 11977 <param name="force" value="false"/>
11644 <param name="test" value="true"/> 11978 <param name="test" value="true"/>
11645 </conditional> 11979 </conditional>
11646 <param name="in" value="IDFileConverter_23_input.mzid"/> 11980 <param name="in" value="IDFileConverter_23_input.mzid"/>
11647 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 11981 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11662 <param name="ignore_proteins_per_peptide" value="false"/> 11996 <param name="ignore_proteins_per_peptide" value="false"/>
11663 <param name="scan_regex" value=""/> 11997 <param name="scan_regex" value=""/>
11664 <param name="no_spectra_data_override" value="false"/> 11998 <param name="no_spectra_data_override" value="false"/>
11665 <param name="no_spectra_references_override" value="false"/> 11999 <param name="no_spectra_references_override" value="false"/>
11666 <param name="add_ionmatch_annotation" value="0.0"/> 12000 <param name="add_ionmatch_annotation" value="0.0"/>
12001 <param name="concatenate_peptides" value="false"/>
12002 <param name="number_of_hits" value="1"/>
11667 <param name="force" value="false"/> 12003 <param name="force" value="false"/>
11668 <param name="test" value="true"/> 12004 <param name="test" value="true"/>
11669 </conditional> 12005 </conditional>
11670 <param name="in" value="IDFileConverter_24_input.pep.xml"/> 12006 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
11671 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 12007 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11686 <param name="ignore_proteins_per_peptide" value="false"/> 12022 <param name="ignore_proteins_per_peptide" value="false"/>
11687 <param name="scan_regex" value=""/> 12023 <param name="scan_regex" value=""/>
11688 <param name="no_spectra_data_override" value="false"/> 12024 <param name="no_spectra_data_override" value="false"/>
11689 <param name="no_spectra_references_override" value="false"/> 12025 <param name="no_spectra_references_override" value="false"/>
11690 <param name="add_ionmatch_annotation" value="0.0"/> 12026 <param name="add_ionmatch_annotation" value="0.0"/>
12027 <param name="concatenate_peptides" value="false"/>
12028 <param name="number_of_hits" value="1"/>
11691 <param name="force" value="false"/> 12029 <param name="force" value="false"/>
11692 <param name="test" value="true"/> 12030 <param name="test" value="true"/>
11693 </conditional> 12031 </conditional>
11694 <param name="in" value="IDFileConverter_25_input.idXML"/> 12032 <param name="in" value="IDFileConverter_25_input.idXML"/>
11695 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> 12033 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>
11710 <param name="ignore_proteins_per_peptide" value="false"/> 12048 <param name="ignore_proteins_per_peptide" value="false"/>
11711 <param name="scan_regex" value=""/> 12049 <param name="scan_regex" value=""/>
11712 <param name="no_spectra_data_override" value="false"/> 12050 <param name="no_spectra_data_override" value="false"/>
11713 <param name="no_spectra_references_override" value="false"/> 12051 <param name="no_spectra_references_override" value="false"/>
11714 <param name="add_ionmatch_annotation" value="0.0"/> 12052 <param name="add_ionmatch_annotation" value="0.0"/>
12053 <param name="concatenate_peptides" value="false"/>
12054 <param name="number_of_hits" value="1"/>
11715 <param name="force" value="false"/> 12055 <param name="force" value="false"/>
11716 <param name="test" value="true"/> 12056 <param name="test" value="true"/>
11717 </conditional> 12057 </conditional>
11718 <param name="in" value="IDFileConverter_26_input.mzid"/> 12058 <param name="in" value="IDFileConverter_26_input.mzid"/>
11719 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 12059 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12060 <param name="out_type" value="idXML"/>
12061 <param name="mz_name" value=""/>
12062 <param name="peptideprophet_analyzed" value="false"/>
12063 <param name="score_type" value="qvalue"/>
12064 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12065 <output name="ctd_out" ftype="xml">
12066 <assert_contents>
12067 <is_valid_xml/>
12068 </assert_contents>
12069 </output>
12070 </test>
12071 <test expect_num_outputs="2">
12072 <conditional name="adv_opts_cond">
12073 <param name="adv_opts_selector" value="advanced"/>
12074 <param name="ignore_proteins_per_peptide" value="false"/>
12075 <param name="scan_regex" value=""/>
12076 <param name="no_spectra_data_override" value="false"/>
12077 <param name="no_spectra_references_override" value="false"/>
12078 <param name="add_ionmatch_annotation" value="0.0"/>
12079 <param name="concatenate_peptides" value="false"/>
12080 <param name="number_of_hits" value="1"/>
12081 <param name="force" value="false"/>
12082 <param name="test" value="true"/>
12083 </conditional>
12084 <param name="in" value="IDFileConverter_27_input.idXML"/>
12085 <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12086 <param name="out_type" value="FASTA"/>
12087 <param name="mz_name" value=""/>
12088 <param name="peptideprophet_analyzed" value="false"/>
12089 <param name="score_type" value="qvalue"/>
12090 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12091 <output name="ctd_out" ftype="xml">
12092 <assert_contents>
12093 <is_valid_xml/>
12094 </assert_contents>
12095 </output>
12096 </test>
12097 <test expect_num_outputs="2">
12098 <conditional name="adv_opts_cond">
12099 <param name="adv_opts_selector" value="advanced"/>
12100 <param name="ignore_proteins_per_peptide" value="false"/>
12101 <param name="scan_regex" value=""/>
12102 <param name="no_spectra_data_override" value="false"/>
12103 <param name="no_spectra_references_override" value="false"/>
12104 <param name="add_ionmatch_annotation" value="0.0"/>
12105 <param name="concatenate_peptides" value="false"/>
12106 <param name="number_of_hits" value="-1"/>
12107 <param name="force" value="false"/>
12108 <param name="test" value="true"/>
12109 </conditional>
12110 <param name="in" value="IDFileConverter_27_input.idXML"/>
12111 <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12112 <param name="out_type" value="FASTA"/>
12113 <param name="mz_name" value=""/>
12114 <param name="peptideprophet_analyzed" value="false"/>
12115 <param name="score_type" value="qvalue"/>
12116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12117 <output name="ctd_out" ftype="xml">
12118 <assert_contents>
12119 <is_valid_xml/>
12120 </assert_contents>
12121 </output>
12122 </test>
12123 <test expect_num_outputs="2">
12124 <conditional name="adv_opts_cond">
12125 <param name="adv_opts_selector" value="advanced"/>
12126 <param name="ignore_proteins_per_peptide" value="false"/>
12127 <param name="scan_regex" value=""/>
12128 <param name="no_spectra_data_override" value="false"/>
12129 <param name="no_spectra_references_override" value="false"/>
12130 <param name="add_ionmatch_annotation" value="0.0"/>
12131 <param name="concatenate_peptides" value="true"/>
12132 <param name="number_of_hits" value="1"/>
12133 <param name="force" value="false"/>
12134 <param name="test" value="true"/>
12135 </conditional>
12136 <param name="in" value="IDFileConverter_27_input.idXML"/>
12137 <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12138 <param name="out_type" value="FASTA"/>
12139 <param name="mz_name" value=""/>
12140 <param name="peptideprophet_analyzed" value="false"/>
12141 <param name="score_type" value="qvalue"/>
12142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12143 <output name="ctd_out" ftype="xml">
12144 <assert_contents>
12145 <is_valid_xml/>
12146 </assert_contents>
12147 </output>
12148 </test>
12149 <test expect_num_outputs="2">
12150 <conditional name="adv_opts_cond">
12151 <param name="adv_opts_selector" value="advanced"/>
12152 <param name="ignore_proteins_per_peptide" value="false"/>
12153 <param name="scan_regex" value=""/>
12154 <param name="no_spectra_data_override" value="false"/>
12155 <param name="no_spectra_references_override" value="false"/>
12156 <param name="add_ionmatch_annotation" value="0.0"/>
12157 <param name="concatenate_peptides" value="true"/>
12158 <param name="number_of_hits" value="2"/>
12159 <param name="force" value="false"/>
12160 <param name="test" value="true"/>
12161 </conditional>
12162 <param name="in" value="IDFileConverter_27_input.idXML"/>
12163 <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
12164 <param name="out_type" value="FASTA"/>
12165 <param name="mz_name" value=""/>
12166 <param name="peptideprophet_analyzed" value="false"/>
12167 <param name="score_type" value="qvalue"/>
12168 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12169 <output name="ctd_out" ftype="xml">
12170 <assert_contents>
12171 <is_valid_xml/>
12172 </assert_contents>
12173 </output>
12174 </test>
12175 <test expect_num_outputs="2">
12176 <conditional name="adv_opts_cond">
12177 <param name="adv_opts_selector" value="advanced"/>
12178 <param name="ignore_proteins_per_peptide" value="false"/>
12179 <param name="scan_regex" value=""/>
12180 <param name="no_spectra_data_override" value="false"/>
12181 <param name="no_spectra_references_override" value="false"/>
12182 <param name="add_ionmatch_annotation" value="0.0"/>
12183 <param name="concatenate_peptides" value="false"/>
12184 <param name="number_of_hits" value="1"/>
12185 <param name="force" value="false"/>
12186 <param name="test" value="true"/>
12187 </conditional>
12188 <param name="in" value="IDFileConverter_31_input.mzid"/>
12189 <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11720 <param name="out_type" value="idXML"/> 12190 <param name="out_type" value="idXML"/>
11721 <param name="mz_name" value=""/> 12191 <param name="mz_name" value=""/>
11722 <param name="peptideprophet_analyzed" value="false"/> 12192 <param name="peptideprophet_analyzed" value="false"/>
11723 <param name="score_type" value="qvalue"/> 12193 <param name="score_type" value="qvalue"/>
11724 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 12194 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11752 <param name="charge" value=":"/> 12222 <param name="charge" value=":"/>
11753 </section> 12223 </section>
11754 <section name="score"> 12224 <section name="score">
11755 <param name="pep" value="0.0"/> 12225 <param name="pep" value="0.0"/>
11756 <param name="prot" value="0.0"/> 12226 <param name="prot" value="0.0"/>
12227 <param name="protgroup" value="0.0"/>
11757 </section> 12228 </section>
11758 <section name="whitelist"> 12229 <section name="whitelist">
11759 <param name="proteins" value="IDFilter_1_input.fas"/> 12230 <param name="proteins" value="IDFilter_1_input.fas"/>
11760 <param name="protein_accessions" value=""/> 12231 <param name="protein_accessions" value=""/>
11761 <param name="ignore_modifications" value="false"/> 12232 <param name="ignore_modifications" value="false"/>
11819 <param name="charge" value=":"/> 12290 <param name="charge" value=":"/>
11820 </section> 12291 </section>
11821 <section name="score"> 12292 <section name="score">
11822 <param name="pep" value="0.0"/> 12293 <param name="pep" value="0.0"/>
11823 <param name="prot" value="0.0"/> 12294 <param name="prot" value="0.0"/>
12295 <param name="protgroup" value="0.0"/>
11824 </section> 12296 </section>
11825 <section name="whitelist"> 12297 <section name="whitelist">
11826 <param name="protein_accessions" value=""/> 12298 <param name="protein_accessions" value=""/>
11827 <param name="ignore_modifications" value="false"/> 12299 <param name="ignore_modifications" value="false"/>
11828 <param name="modifications" value=""/> 12300 <param name="modifications" value=""/>
11886 <param name="charge" value=":"/> 12358 <param name="charge" value=":"/>
11887 </section> 12359 </section>
11888 <section name="score"> 12360 <section name="score">
11889 <param name="pep" value="0.0"/> 12361 <param name="pep" value="0.0"/>
11890 <param name="prot" value="0.0"/> 12362 <param name="prot" value="0.0"/>
12363 <param name="protgroup" value="0.0"/>
11891 </section> 12364 </section>
11892 <section name="whitelist"> 12365 <section name="whitelist">
11893 <param name="protein_accessions" value=""/> 12366 <param name="protein_accessions" value=""/>
11894 <param name="ignore_modifications" value="false"/> 12367 <param name="ignore_modifications" value="false"/>
11895 <param name="modifications" value=""/> 12368 <param name="modifications" value=""/>
11952 <param name="charge" value=":"/> 12425 <param name="charge" value=":"/>
11953 </section> 12426 </section>
11954 <section name="score"> 12427 <section name="score">
11955 <param name="pep" value="32.0"/> 12428 <param name="pep" value="32.0"/>
11956 <param name="prot" value="25.0"/> 12429 <param name="prot" value="25.0"/>
12430 <param name="protgroup" value="0.0"/>
11957 </section> 12431 </section>
11958 <section name="whitelist"> 12432 <section name="whitelist">
11959 <param name="protein_accessions" value=""/> 12433 <param name="protein_accessions" value=""/>
11960 <param name="ignore_modifications" value="false"/> 12434 <param name="ignore_modifications" value="false"/>
11961 <param name="modifications" value=""/> 12435 <param name="modifications" value=""/>
12018 <param name="charge" value=":"/> 12492 <param name="charge" value=":"/>
12019 </section> 12493 </section>
12020 <section name="score"> 12494 <section name="score">
12021 <param name="pep" value="32.0"/> 12495 <param name="pep" value="32.0"/>
12022 <param name="prot" value="0.0"/> 12496 <param name="prot" value="0.0"/>
12497 <param name="protgroup" value="0.0"/>
12023 </section> 12498 </section>
12024 <section name="whitelist"> 12499 <section name="whitelist">
12025 <param name="protein_accessions" value=""/> 12500 <param name="protein_accessions" value=""/>
12026 <param name="ignore_modifications" value="false"/> 12501 <param name="ignore_modifications" value="false"/>
12027 <param name="modifications" value=""/> 12502 <param name="modifications" value=""/>
12084 <param name="charge" value=":"/> 12559 <param name="charge" value=":"/>
12085 </section> 12560 </section>
12086 <section name="score"> 12561 <section name="score">
12087 <param name="pep" value="0.0"/> 12562 <param name="pep" value="0.0"/>
12088 <param name="prot" value="25.0"/> 12563 <param name="prot" value="25.0"/>
12564 <param name="protgroup" value="0.0"/>
12089 </section> 12565 </section>
12090 <section name="whitelist"> 12566 <section name="whitelist">
12091 <param name="protein_accessions" value=""/> 12567 <param name="protein_accessions" value=""/>
12092 <param name="ignore_modifications" value="false"/> 12568 <param name="ignore_modifications" value="false"/>
12093 <param name="modifications" value=""/> 12569 <param name="modifications" value=""/>
12150 <param name="charge" value=":"/> 12626 <param name="charge" value=":"/>
12151 </section> 12627 </section>
12152 <section name="score"> 12628 <section name="score">
12153 <param name="pep" value="0.0"/> 12629 <param name="pep" value="0.0"/>
12154 <param name="prot" value="25.0"/> 12630 <param name="prot" value="25.0"/>
12631 <param name="protgroup" value="0.0"/>
12155 </section> 12632 </section>
12156 <section name="whitelist"> 12633 <section name="whitelist">
12157 <param name="protein_accessions" value=""/> 12634 <param name="protein_accessions" value=""/>
12158 <param name="ignore_modifications" value="false"/> 12635 <param name="ignore_modifications" value="false"/>
12159 <param name="modifications" value=""/> 12636 <param name="modifications" value=""/>
12216 <param name="charge" value=":"/> 12693 <param name="charge" value=":"/>
12217 </section> 12694 </section>
12218 <section name="score"> 12695 <section name="score">
12219 <param name="pep" value="0.0"/> 12696 <param name="pep" value="0.0"/>
12220 <param name="prot" value="0.0"/> 12697 <param name="prot" value="0.0"/>
12698 <param name="protgroup" value="0.0"/>
12221 </section> 12699 </section>
12222 <section name="whitelist"> 12700 <section name="whitelist">
12223 <param name="protein_accessions" value=""/> 12701 <param name="protein_accessions" value=""/>
12224 <param name="ignore_modifications" value="false"/> 12702 <param name="ignore_modifications" value="false"/>
12225 <param name="modifications" value=""/> 12703 <param name="modifications" value=""/>
12282 <param name="charge" value=":"/> 12760 <param name="charge" value=":"/>
12283 </section> 12761 </section>
12284 <section name="score"> 12762 <section name="score">
12285 <param name="pep" value="0.0"/> 12763 <param name="pep" value="0.0"/>
12286 <param name="prot" value="0.0"/> 12764 <param name="prot" value="0.0"/>
12765 <param name="protgroup" value="0.0"/>
12287 </section> 12766 </section>
12288 <section name="whitelist"> 12767 <section name="whitelist">
12289 <param name="protein_accessions" value=""/> 12768 <param name="protein_accessions" value=""/>
12290 <param name="ignore_modifications" value="false"/> 12769 <param name="ignore_modifications" value="false"/>
12291 <param name="modifications" value=""/> 12770 <param name="modifications" value=""/>
12348 <param name="charge" value=":"/> 12827 <param name="charge" value=":"/>
12349 </section> 12828 </section>
12350 <section name="score"> 12829 <section name="score">
12351 <param name="pep" value="0.0"/> 12830 <param name="pep" value="0.0"/>
12352 <param name="prot" value="0.0"/> 12831 <param name="prot" value="0.0"/>
12832 <param name="protgroup" value="0.0"/>
12353 </section> 12833 </section>
12354 <section name="whitelist"> 12834 <section name="whitelist">
12355 <param name="protein_accessions" value=""/> 12835 <param name="protein_accessions" value=""/>
12356 <param name="ignore_modifications" value="false"/> 12836 <param name="ignore_modifications" value="false"/>
12357 <param name="modifications" value=""/> 12837 <param name="modifications" value=""/>
12414 <param name="charge" value=":"/> 12894 <param name="charge" value=":"/>
12415 </section> 12895 </section>
12416 <section name="score"> 12896 <section name="score">
12417 <param name="pep" value="0.05"/> 12897 <param name="pep" value="0.05"/>
12418 <param name="prot" value="0.0"/> 12898 <param name="prot" value="0.0"/>
12899 <param name="protgroup" value="0.0"/>
12419 </section> 12900 </section>
12420 <section name="whitelist"> 12901 <section name="whitelist">
12421 <param name="protein_accessions" value=""/> 12902 <param name="protein_accessions" value=""/>
12422 <param name="ignore_modifications" value="false"/> 12903 <param name="ignore_modifications" value="false"/>
12423 <param name="modifications" value=""/> 12904 <param name="modifications" value=""/>
12480 <param name="charge" value=":"/> 12961 <param name="charge" value=":"/>
12481 </section> 12962 </section>
12482 <section name="score"> 12963 <section name="score">
12483 <param name="pep" value="0.0"/> 12964 <param name="pep" value="0.0"/>
12484 <param name="prot" value="0.3"/> 12965 <param name="prot" value="0.3"/>
12966 <param name="protgroup" value="0.0"/>
12485 </section> 12967 </section>
12486 <section name="whitelist"> 12968 <section name="whitelist">
12487 <param name="protein_accessions" value=""/> 12969 <param name="protein_accessions" value=""/>
12488 <param name="ignore_modifications" value="false"/> 12970 <param name="ignore_modifications" value="false"/>
12489 <param name="modifications" value=""/> 12971 <param name="modifications" value=""/>
12546 <param name="charge" value=":"/> 13028 <param name="charge" value=":"/>
12547 </section> 13029 </section>
12548 <section name="score"> 13030 <section name="score">
12549 <param name="pep" value="0.0"/> 13031 <param name="pep" value="0.0"/>
12550 <param name="prot" value="0.0"/> 13032 <param name="prot" value="0.0"/>
13033 <param name="protgroup" value="0.0"/>
12551 </section> 13034 </section>
12552 <section name="whitelist"> 13035 <section name="whitelist">
12553 <param name="protein_accessions" value=""/> 13036 <param name="protein_accessions" value=""/>
12554 <param name="ignore_modifications" value="false"/> 13037 <param name="ignore_modifications" value="false"/>
12555 <param name="modifications" value=""/> 13038 <param name="modifications" value=""/>
12612 <param name="charge" value=":"/> 13095 <param name="charge" value=":"/>
12613 </section> 13096 </section>
12614 <section name="score"> 13097 <section name="score">
12615 <param name="pep" value="0.0"/> 13098 <param name="pep" value="0.0"/>
12616 <param name="prot" value="0.0"/> 13099 <param name="prot" value="0.0"/>
13100 <param name="protgroup" value="0.0"/>
12617 </section> 13101 </section>
12618 <section name="whitelist"> 13102 <section name="whitelist">
12619 <param name="protein_accessions" value=""/> 13103 <param name="protein_accessions" value=""/>
12620 <param name="ignore_modifications" value="false"/> 13104 <param name="ignore_modifications" value="false"/>
12621 <param name="modifications" value=""/> 13105 <param name="modifications" value=""/>
12679 <param name="charge" value=":"/> 13163 <param name="charge" value=":"/>
12680 </section> 13164 </section>
12681 <section name="score"> 13165 <section name="score">
12682 <param name="pep" value="0.0"/> 13166 <param name="pep" value="0.0"/>
12683 <param name="prot" value="0.0"/> 13167 <param name="prot" value="0.0"/>
13168 <param name="protgroup" value="0.0"/>
12684 </section> 13169 </section>
12685 <section name="whitelist"> 13170 <section name="whitelist">
12686 <param name="protein_accessions" value=""/> 13171 <param name="protein_accessions" value=""/>
12687 <param name="ignore_modifications" value="false"/> 13172 <param name="ignore_modifications" value="false"/>
12688 <param name="modifications" value=""/> 13173 <param name="modifications" value=""/>
12746 <param name="charge" value=":"/> 13231 <param name="charge" value=":"/>
12747 </section> 13232 </section>
12748 <section name="score"> 13233 <section name="score">
12749 <param name="pep" value="0.0"/> 13234 <param name="pep" value="0.0"/>
12750 <param name="prot" value="0.0"/> 13235 <param name="prot" value="0.0"/>
13236 <param name="protgroup" value="0.0"/>
12751 </section> 13237 </section>
12752 <section name="whitelist"> 13238 <section name="whitelist">
12753 <param name="protein_accessions" value=""/> 13239 <param name="protein_accessions" value=""/>
12754 <param name="ignore_modifications" value="false"/> 13240 <param name="ignore_modifications" value="false"/>
12755 <param name="modifications" value=""/> 13241 <param name="modifications" value=""/>
12813 <param name="charge" value=":"/> 13299 <param name="charge" value=":"/>
12814 </section> 13300 </section>
12815 <section name="score"> 13301 <section name="score">
12816 <param name="pep" value="0.0"/> 13302 <param name="pep" value="0.0"/>
12817 <param name="prot" value="0.0"/> 13303 <param name="prot" value="0.0"/>
13304 <param name="protgroup" value="0.0"/>
12818 </section> 13305 </section>
12819 <section name="whitelist"> 13306 <section name="whitelist">
12820 <param name="protein_accessions" value=""/> 13307 <param name="protein_accessions" value=""/>
12821 <param name="ignore_modifications" value="false"/> 13308 <param name="ignore_modifications" value="false"/>
12822 <param name="modifications" value=""/> 13309 <param name="modifications" value=""/>
12880 <param name="charge" value=":"/> 13367 <param name="charge" value=":"/>
12881 </section> 13368 </section>
12882 <section name="score"> 13369 <section name="score">
12883 <param name="pep" value="0.0"/> 13370 <param name="pep" value="0.0"/>
12884 <param name="prot" value="0.0"/> 13371 <param name="prot" value="0.0"/>
13372 <param name="protgroup" value="0.0"/>
12885 </section> 13373 </section>
12886 <section name="whitelist"> 13374 <section name="whitelist">
12887 <param name="protein_accessions" value=""/> 13375 <param name="protein_accessions" value=""/>
12888 <param name="ignore_modifications" value="false"/> 13376 <param name="ignore_modifications" value="false"/>
12889 <param name="modifications" value=""/> 13377 <param name="modifications" value=""/>
12947 <param name="charge" value=":"/> 13435 <param name="charge" value=":"/>
12948 </section> 13436 </section>
12949 <section name="score"> 13437 <section name="score">
12950 <param name="pep" value="0.0"/> 13438 <param name="pep" value="0.0"/>
12951 <param name="prot" value="0.0"/> 13439 <param name="prot" value="0.0"/>
13440 <param name="protgroup" value="0.0"/>
12952 </section> 13441 </section>
12953 <section name="whitelist"> 13442 <section name="whitelist">
12954 <param name="protein_accessions" value=""/> 13443 <param name="protein_accessions" value=""/>
12955 <param name="ignore_modifications" value="false"/> 13444 <param name="ignore_modifications" value="false"/>
12956 <param name="modifications" value=""/> 13445 <param name="modifications" value=""/>
13013 <param name="charge" value=":"/> 13502 <param name="charge" value=":"/>
13014 </section> 13503 </section>
13015 <section name="score"> 13504 <section name="score">
13016 <param name="pep" value="0.0"/> 13505 <param name="pep" value="0.0"/>
13017 <param name="prot" value="0.0"/> 13506 <param name="prot" value="0.0"/>
13507 <param name="protgroup" value="0.0"/>
13018 </section> 13508 </section>
13019 <section name="whitelist"> 13509 <section name="whitelist">
13020 <param name="protein_accessions" value=""/> 13510 <param name="protein_accessions" value=""/>
13021 <param name="ignore_modifications" value="false"/> 13511 <param name="ignore_modifications" value="false"/>
13022 <param name="modifications" value=""/> 13512 <param name="modifications" value=""/>
13079 <param name="charge" value=":"/> 13569 <param name="charge" value=":"/>
13080 </section> 13570 </section>
13081 <section name="score"> 13571 <section name="score">
13082 <param name="pep" value="0.0"/> 13572 <param name="pep" value="0.0"/>
13083 <param name="prot" value="0.0"/> 13573 <param name="prot" value="0.0"/>
13574 <param name="protgroup" value="0.0"/>
13084 </section> 13575 </section>
13085 <section name="whitelist"> 13576 <section name="whitelist">
13086 <param name="protein_accessions" value=""/> 13577 <param name="protein_accessions" value=""/>
13087 <param name="ignore_modifications" value="false"/> 13578 <param name="ignore_modifications" value="false"/>
13088 <param name="modifications" value=""/> 13579 <param name="modifications" value=""/>
13145 <param name="charge" value=":"/> 13636 <param name="charge" value=":"/>
13146 </section> 13637 </section>
13147 <section name="score"> 13638 <section name="score">
13148 <param name="pep" value="0.0"/> 13639 <param name="pep" value="0.0"/>
13149 <param name="prot" value="0.0"/> 13640 <param name="prot" value="0.0"/>
13641 <param name="protgroup" value="0.0"/>
13150 </section> 13642 </section>
13151 <section name="whitelist"> 13643 <section name="whitelist">
13152 <param name="protein_accessions" value=""/> 13644 <param name="protein_accessions" value=""/>
13153 <param name="ignore_modifications" value="false"/> 13645 <param name="ignore_modifications" value="false"/>
13154 <param name="modifications" value=""/> 13646 <param name="modifications" value=""/>
13211 <param name="charge" value=":"/> 13703 <param name="charge" value=":"/>
13212 </section> 13704 </section>
13213 <section name="score"> 13705 <section name="score">
13214 <param name="pep" value="0.0"/> 13706 <param name="pep" value="0.0"/>
13215 <param name="prot" value="0.0"/> 13707 <param name="prot" value="0.0"/>
13708 <param name="protgroup" value="0.0"/>
13216 </section> 13709 </section>
13217 <section name="whitelist"> 13710 <section name="whitelist">
13218 <param name="protein_accessions" value=""/> 13711 <param name="protein_accessions" value=""/>
13219 <param name="ignore_modifications" value="false"/> 13712 <param name="ignore_modifications" value="false"/>
13220 <param name="modifications" value=""/> 13713 <param name="modifications" value=""/>
13277 <param name="charge" value=":"/> 13770 <param name="charge" value=":"/>
13278 </section> 13771 </section>
13279 <section name="score"> 13772 <section name="score">
13280 <param name="pep" value="0.0"/> 13773 <param name="pep" value="0.0"/>
13281 <param name="prot" value="0.0"/> 13774 <param name="prot" value="0.0"/>
13775 <param name="protgroup" value="0.0"/>
13776 </section>
13777 <section name="whitelist">
13778 <param name="protein_accessions" value=""/>
13779 <param name="ignore_modifications" value="false"/>
13780 <param name="modifications" value=""/>
13781 </section>
13782 <section name="blacklist">
13783 <param name="protein_accessions" value=""/>
13784 <param name="ignore_modifications" value="false"/>
13785 <param name="modifications" value=""/>
13786 </section>
13787 <section name="in_silico_digestion">
13788 <param name="enzyme" value="Trypsin"/>
13789 <param name="specificity" value="full"/>
13790 <param name="missed_cleavages" value="-1"/>
13791 <param name="methionine_cleavage" value="false"/>
13792 </section>
13793 <section name="missed_cleavages">
13794 <param name="number_of_missed_cleavages" value=":"/>
13795 <param name="enzyme" value="Trypsin"/>
13796 </section>
13797 <section name="rt">
13798 <param name="p_value" value="0.0"/>
13799 <param name="p_value_1st_dim" value="0.0"/>
13800 </section>
13801 <section name="mz">
13802 <param name="error" value="-1.0"/>
13803 <param name="unit" value="ppm"/>
13804 </section>
13805 <section name="best">
13806 <param name="n_peptide_hits" value="0"/>
13807 <param name="n_protein_hits" value="0"/>
13808 <param name="strict" value="false"/>
13809 <param name="n_to_m_peptide_hits" value=":"/>
13810 </section>
13811 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13812 <output name="ctd_out" ftype="xml">
13813 <assert_contents>
13814 <is_valid_xml/>
13815 </assert_contents>
13816 </output>
13817 </test>
13818 <test expect_num_outputs="2">
13819 <conditional name="adv_opts_cond">
13820 <param name="adv_opts_selector" value="advanced"/>
13821 <param name="remove_duplicate_psm" value="false"/>
13822 <param name="remove_peptide_hits_by_metavalue" value=""/>
13823 <param name="force" value="false"/>
13824 <param name="test" value="true"/>
13825 </conditional>
13826 <param name="in" value="IDMapper_2_output.consensusXML"/>
13827 <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13828 <param name="var_mods" value="false"/>
13829 <param name="remove_shared_peptides" value="false"/>
13830 <param name="keep_unreferenced_protein_hits" value="false"/>
13831 <param name="remove_decoys" value="false"/>
13832 <param name="delete_unreferenced_peptide_hits" value="false"/>
13833 <section name="precursor">
13834 <param name="rt" value=":"/>
13835 <param name="mz" value=":"/>
13836 <param name="length" value=":"/>
13837 <param name="charge" value=":"/>
13838 </section>
13839 <section name="score">
13840 <param name="pep" value="0.0"/>
13841 <param name="prot" value="0.0"/>
13842 <param name="protgroup" value="0.0"/>
13843 </section>
13844 <section name="whitelist">
13845 <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
13846 <param name="ignore_modifications" value="false"/>
13847 <param name="modifications" value=""/>
13848 </section>
13849 <section name="blacklist">
13850 <param name="protein_accessions" value=""/>
13851 <param name="ignore_modifications" value="false"/>
13852 <param name="modifications" value=""/>
13853 </section>
13854 <section name="in_silico_digestion">
13855 <param name="enzyme" value="Trypsin"/>
13856 <param name="specificity" value="full"/>
13857 <param name="missed_cleavages" value="-1"/>
13858 <param name="methionine_cleavage" value="false"/>
13859 </section>
13860 <section name="missed_cleavages">
13861 <param name="number_of_missed_cleavages" value=":"/>
13862 <param name="enzyme" value="Trypsin"/>
13863 </section>
13864 <section name="rt">
13865 <param name="p_value" value="0.0"/>
13866 <param name="p_value_1st_dim" value="0.0"/>
13867 </section>
13868 <section name="mz">
13869 <param name="error" value="-1.0"/>
13870 <param name="unit" value="ppm"/>
13871 </section>
13872 <section name="best">
13873 <param name="n_peptide_hits" value="0"/>
13874 <param name="n_protein_hits" value="0"/>
13875 <param name="strict" value="false"/>
13876 <param name="n_to_m_peptide_hits" value=":"/>
13877 </section>
13878 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13879 <output name="ctd_out" ftype="xml">
13880 <assert_contents>
13881 <is_valid_xml/>
13882 </assert_contents>
13883 </output>
13884 </test>
13885 <test expect_num_outputs="2">
13886 <conditional name="adv_opts_cond">
13887 <param name="adv_opts_selector" value="advanced"/>
13888 <param name="remove_duplicate_psm" value="false"/>
13889 <param name="remove_peptide_hits_by_metavalue" value=""/>
13890 <param name="force" value="false"/>
13891 <param name="test" value="true"/>
13892 </conditional>
13893 <param name="in" value="Epifany_3_out.consensusXML"/>
13894 <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13895 <param name="var_mods" value="false"/>
13896 <param name="remove_shared_peptides" value="false"/>
13897 <param name="keep_unreferenced_protein_hits" value="false"/>
13898 <param name="remove_decoys" value="false"/>
13899 <param name="delete_unreferenced_peptide_hits" value="false"/>
13900 <section name="precursor">
13901 <param name="rt" value=":"/>
13902 <param name="mz" value=":"/>
13903 <param name="length" value=":"/>
13904 <param name="charge" value=":"/>
13905 </section>
13906 <section name="score">
13907 <param name="pep" value="0.0"/>
13908 <param name="prot" value="0.0"/>
13909 <param name="protgroup" value="0.99"/>
13282 </section> 13910 </section>
13283 <section name="whitelist"> 13911 <section name="whitelist">
13284 <param name="protein_accessions" value=""/> 13912 <param name="protein_accessions" value=""/>
13285 <param name="ignore_modifications" value="false"/> 13913 <param name="ignore_modifications" value="false"/>
13286 <param name="modifications" value=""/> 13914 <param name="modifications" value=""/>
13880 <param name="force" value="false"/> 14508 <param name="force" value="false"/>
13881 <param name="test" value="true"/> 14509 <param name="test" value="true"/>
13882 </conditional> 14510 </conditional>
13883 <param name="in" value="IDFileConverter_12_output.idXML"/> 14511 <param name="in" value="IDFileConverter_12_output.idXML"/>
13884 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 14512 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14513 <param name="proteins" value="false"/>
13885 <param name="new_score" value="Percolator_PEP"/> 14514 <param name="new_score" value="Percolator_PEP"/>
13886 <param name="new_score_orientation" value="lower_better"/> 14515 <param name="new_score_orientation" value="lower_better"/>
13887 <param name="new_score_type" value="Posterior Error Probability"/> 14516 <param name="new_score_type" value="Posterior Error Probability"/>
13888 <param name="old_score" value="Percolator_qvalue"/> 14517 <param name="old_score" value="Percolator_qvalue"/>
13889 <param name="proteins" value="false"/>
13890 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 14518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13891 <output name="ctd_out" ftype="xml"> 14519 <output name="ctd_out" ftype="xml">
13892 <assert_contents> 14520 <assert_contents>
13893 <is_valid_xml/> 14521 <is_valid_xml/>
13894 </assert_contents> 14522 </assert_contents>
13900 <param name="force" value="false"/> 14528 <param name="force" value="false"/>
13901 <param name="test" value="true"/> 14529 <param name="test" value="true"/>
13902 </conditional> 14530 </conditional>
13903 <param name="in" value="IDScoreSwitcher_2_input.idXML"/> 14531 <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
13904 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 14532 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14533 <param name="proteins" value="true"/>
13905 <param name="new_score" value="Posterior Probability_score"/> 14534 <param name="new_score" value="Posterior Probability_score"/>
13906 <param name="new_score_orientation" value="higher_better"/> 14535 <param name="new_score_orientation" value="higher_better"/>
13907 <param name="new_score_type" value="Posterior Probability"/> 14536 <param name="new_score_type" value="Posterior Probability"/>
13908 <param name="old_score" value=""/> 14537 <param name="old_score" value=""/>
13909 <param name="proteins" value="true"/>
13910 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 14538 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13911 <output name="ctd_out" ftype="xml"> 14539 <output name="ctd_out" ftype="xml">
13912 <assert_contents> 14540 <assert_contents>
13913 <is_valid_xml/> 14541 <is_valid_xml/>
13914 </assert_contents> 14542 </assert_contents>
14451 </output> 15079 </output>
14452 </test> 15080 </test>
14453 </xml> 15081 </xml>
14454 <xml name="autotest_LabeledEval"> 15082 <xml name="autotest_LabeledEval">
14455 </xml> 15083 </xml>
14456 <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
14457 <test expect_num_outputs="2">
14458 <conditional name="adv_opts_cond">
14459 <param name="adv_opts_selector" value="advanced"/>
14460 <param name="force" value="false"/>
14461 <param name="test" value="true"/>
14462 </conditional>
14463 <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/>
14464 <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
14465 <section name="algorithm">
14466 <param name="signal_to_noise" value="1.0"/>
14467 <param name="spacing_difference_gap" value="4.0"/>
14468 <param name="spacing_difference" value="1.5"/>
14469 <param name="missing" value="1"/>
14470 <param name="ms_levels" value="1"/>
14471 <param name="report_FWHM" value="false"/>
14472 <param name="report_FWHM_unit" value="relative"/>
14473 <section name="SignalToNoise">
14474 <param name="max_intensity" value="-1"/>
14475 <param name="auto_max_stdev_factor" value="3.0"/>
14476 <param name="auto_max_percentile" value="95"/>
14477 <param name="auto_mode" value="0"/>
14478 <param name="win_len" value="200.0"/>
14479 <param name="bin_count" value="30"/>
14480 <param name="min_required_elements" value="10"/>
14481 <param name="noise_for_empty_window" value="1e+20"/>
14482 <param name="write_log_messages" value="true"/>
14483 </section>
14484 </section>
14485 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14486 <output name="ctd_out" ftype="xml">
14487 <assert_contents>
14488 <is_valid_xml/>
14489 </assert_contents>
14490 </output>
14491 </test>
14492 </xml>
14493 <xml name="autotest_LowMemPeakPickerHiRes">
14494 <test expect_num_outputs="2">
14495 <conditional name="adv_opts_cond">
14496 <param name="adv_opts_selector" value="advanced"/>
14497 <param name="force" value="false"/>
14498 <param name="test" value="true"/>
14499 </conditional>
14500 <param name="in" value="PeakPickerHiRes_input.mzML"/>
14501 <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
14502 <section name="algorithm">
14503 <param name="signal_to_noise" value="1.0"/>
14504 <param name="spacing_difference_gap" value="4.0"/>
14505 <param name="spacing_difference" value="1.5"/>
14506 <param name="missing" value="1"/>
14507 <param name="ms_levels" value="1"/>
14508 <param name="report_FWHM" value="false"/>
14509 <param name="report_FWHM_unit" value="relative"/>
14510 <section name="SignalToNoise">
14511 <param name="max_intensity" value="-1"/>
14512 <param name="auto_max_stdev_factor" value="3.0"/>
14513 <param name="auto_max_percentile" value="95"/>
14514 <param name="auto_mode" value="0"/>
14515 <param name="win_len" value="200.0"/>
14516 <param name="bin_count" value="30"/>
14517 <param name="min_required_elements" value="10"/>
14518 <param name="noise_for_empty_window" value="1e+20"/>
14519 <param name="write_log_messages" value="true"/>
14520 </section>
14521 </section>
14522 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14523 <output name="ctd_out" ftype="xml">
14524 <assert_contents>
14525 <is_valid_xml/>
14526 </assert_contents>
14527 </output>
14528 </test>
14529 </xml>
14530 <xml name="autotest_LuciphorAdapter"> 15084 <xml name="autotest_LuciphorAdapter">
14531 <test expect_num_outputs="2"> 15085 <test expect_num_outputs="2">
14532 <conditional name="adv_opts_cond"> 15086 <conditional name="adv_opts_cond">
14533 <param name="adv_opts_selector" value="advanced"/> 15087 <param name="adv_opts_selector" value="advanced"/>
14534 <param name="force" value="false"/> 15088 <param name="force" value="false"/>
14886 <param name="interpolation_type" value="cspline"/> 15440 <param name="interpolation_type" value="cspline"/>
14887 <param name="extrapolation_type" value="two-point-linear"/> 15441 <param name="extrapolation_type" value="two-point-linear"/>
14888 </section> 15442 </section>
14889 </section> 15443 </section>
14890 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> 15444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15445 <output name="ctd_out" ftype="xml">
15446 <assert_contents>
15447 <is_valid_xml/>
15448 </assert_contents>
15449 </output>
15450 </test>
15451 <test expect_num_outputs="3">
15452 <conditional name="adv_opts_cond">
15453 <param name="adv_opts_selector" value="advanced"/>
15454 <param name="force" value="true"/>
15455 <param name="test" value="true"/>
15456 </conditional>
15457 <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
15458 <output_collection name="out" count="1"/>
15459 <output_collection name="trafo_out" count="1"/>
15460 <section name="reference">
15461 <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
15462 <param name="index" value="0"/>
15463 </section>
15464 <section name="algorithm">
15465 <param name="score_cutoff" value="false"/>
15466 <param name="min_score" value="0.05"/>
15467 <param name="min_run_occur" value="2"/>
15468 <param name="max_rt_shift" value="0.5"/>
15469 <param name="use_unassigned_peptides" value="true"/>
15470 <param name="use_feature_rt" value="false"/>
15471 </section>
15472 <section name="model">
15473 <param name="type" value="b_spline"/>
15474 <section name="linear">
15475 <param name="symmetric_regression" value="false"/>
15476 <param name="x_weight" value=""/>
15477 <param name="y_weight" value=""/>
15478 <param name="x_datum_min" value="1e-15"/>
15479 <param name="x_datum_max" value="1000000000000000.0"/>
15480 <param name="y_datum_min" value="1e-15"/>
15481 <param name="y_datum_max" value="1000000000000000.0"/>
15482 </section>
15483 <section name="b_spline">
15484 <param name="wavelength" value="0.0"/>
15485 <param name="num_nodes" value="5"/>
15486 <param name="extrapolate" value="linear"/>
15487 <param name="boundary_condition" value="2"/>
15488 </section>
15489 <section name="lowess">
15490 <param name="span" value="0.666666666666667"/>
15491 <param name="num_iterations" value="3"/>
15492 <param name="delta" value="-1.0"/>
15493 <param name="interpolation_type" value="cspline"/>
15494 <param name="extrapolation_type" value="four-point-linear"/>
15495 </section>
15496 <section name="interpolated">
15497 <param name="interpolation_type" value="cspline"/>
15498 <param name="extrapolation_type" value="two-point-linear"/>
15499 </section>
15500 </section>
15501 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
14891 <output name="ctd_out" ftype="xml"> 15502 <output name="ctd_out" ftype="xml">
14892 <assert_contents> 15503 <assert_contents>
14893 <is_valid_xml/> 15504 <is_valid_xml/>
14894 </assert_contents> 15505 </assert_contents>
14895 </output> 15506 </output>
15279 <assert_contents> 15890 <assert_contents>
15280 <is_valid_xml/> 15891 <is_valid_xml/>
15281 </assert_contents> 15892 </assert_contents>
15282 </output> 15893 </output>
15283 </test> 15894 </test>
15895 <test expect_num_outputs="2">
15896 <conditional name="adv_opts_cond">
15897 <param name="adv_opts_selector" value="advanced"/>
15898 <param name="force" value="false"/>
15899 <param name="test" value="true"/>
15900 </conditional>
15901 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15902 <output_collection name="out" count="3"/>
15903 <section name="algorithm">
15904 <param name="model_type" value="b_spline"/>
15905 <section name="model">
15906 <param name="type" value="b_spline"/>
15907 <section name="linear">
15908 <param name="symmetric_regression" value="false"/>
15909 <param name="x_weight" value=""/>
15910 <param name="y_weight" value=""/>
15911 <param name="x_datum_min" value="1e-15"/>
15912 <param name="x_datum_max" value="1000000000000000.0"/>
15913 <param name="y_datum_min" value="1e-15"/>
15914 <param name="y_datum_max" value="1000000000000000.0"/>
15915 </section>
15916 <section name="b_spline">
15917 <param name="wavelength" value="0.0"/>
15918 <param name="num_nodes" value="5"/>
15919 <param name="extrapolate" value="linear"/>
15920 <param name="boundary_condition" value="2"/>
15921 </section>
15922 <section name="lowess">
15923 <param name="span" value="0.666666666666667"/>
15924 <param name="num_iterations" value="3"/>
15925 <param name="delta" value="-1.0"/>
15926 <param name="interpolation_type" value="cspline"/>
15927 <param name="extrapolation_type" value="four-point-linear"/>
15928 </section>
15929 <section name="interpolated">
15930 <param name="interpolation_type" value="cspline"/>
15931 <param name="extrapolation_type" value="two-point-linear"/>
15932 </section>
15933 </section>
15934 <section name="align_algorithm">
15935 <param name="score_cutoff" value="false"/>
15936 <param name="min_score" value="0.05"/>
15937 <param name="min_run_occur" value="2"/>
15938 <param name="max_rt_shift" value="0.5"/>
15939 <param name="use_unassigned_peptides" value="true"/>
15940 <param name="use_feature_rt" value="true"/>
15941 </section>
15942 </section>
15943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15944 <output name="ctd_out" ftype="xml">
15945 <assert_contents>
15946 <is_valid_xml/>
15947 </assert_contents>
15948 </output>
15949 </test>
15284 </xml> 15950 </xml>
15285 <xml name="autotest_MapNormalizer"> 15951 <xml name="autotest_MapNormalizer">
15286 <test expect_num_outputs="2"> 15952 <test expect_num_outputs="2">
15287 <conditional name="adv_opts_cond"> 15953 <conditional name="adv_opts_cond">
15288 <param name="adv_opts_selector" value="advanced"/> 15954 <param name="adv_opts_selector" value="advanced"/>
15649 <param name="adv_opts_selector" value="advanced"/> 16315 <param name="adv_opts_selector" value="advanced"/>
15650 <param name="force" value="false"/> 16316 <param name="force" value="false"/>
15651 <param name="test" value="true"/> 16317 <param name="test" value="true"/>
15652 </conditional> 16318 </conditional>
15653 <param name="in" value="MascotAdapter_1_input.mzData"/> 16319 <param name="in" value="MascotAdapter_1_input.mzData"/>
15654 <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 16320 <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
15655 <param name="mascot_in" value="true"/> 16321 <param name="out_type" value="mgf"/>
15656 <param name="mascot_out" value="false"/>
15657 <param name="instrument" value="ESI-TRAP"/> 16322 <param name="instrument" value="ESI-TRAP"/>
15658 <param name="precursor_mass_tolerance" value="1.3"/> 16323 <param name="precursor_mass_tolerance" value="1.3"/>
15659 <param name="peak_mass_tolerance" value="0.3"/> 16324 <param name="peak_mass_tolerance" value="0.3"/>
15660 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> 16325 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
15661 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/> 16326 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
15689 <param name="force" value="false"/> 16354 <param name="force" value="false"/>
15690 <param name="test" value="true"/> 16355 <param name="test" value="true"/>
15691 </conditional> 16356 </conditional>
15692 <param name="in" value="MascotAdapter_2_input.mascotXML"/> 16357 <param name="in" value="MascotAdapter_2_input.mascotXML"/>
15693 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 16358 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
15694 <param name="mascot_in" value="false"/> 16359 <param name="out_type" value="idXML"/>
15695 <param name="mascot_out" value="true"/>
15696 <param name="instrument" value="Default"/> 16360 <param name="instrument" value="Default"/>
15697 <param name="precursor_mass_tolerance" value="2.0"/> 16361 <param name="precursor_mass_tolerance" value="2.0"/>
15698 <param name="peak_mass_tolerance" value="1.0"/> 16362 <param name="peak_mass_tolerance" value="1.0"/>
15699 <param name="taxonomy" value="All entries"/> 16363 <param name="taxonomy" value="All entries"/>
15700 <param name="modifications" value=""/> 16364 <param name="modifications" value=""/>
15728 <conditional name="adv_opts_cond"> 16392 <conditional name="adv_opts_cond">
15729 <param name="adv_opts_selector" value="advanced"/> 16393 <param name="adv_opts_selector" value="advanced"/>
15730 <param name="force" value="false"/> 16394 <param name="force" value="false"/>
15731 <param name="test" value="true"/> 16395 <param name="test" value="true"/>
15732 </conditional> 16396 </conditional>
15733 <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/> 16397 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
15734 <param name="in_seq" value=""/> 16398 <param name="in_seq" value=""/>
15735 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/> 16399 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
15736 <param name="charge" value="0 1"/> 16400 <param name="charge" value="0 1"/>
15737 <param name="format" value="table"/> 16401 <param name="format" value="table"/>
15738 <param name="average_mass" value="false"/> 16402 <param name="average_mass" value="false"/>
15739 <param name="fragment_type" value="full"/> 16403 <param name="fragment_type" value="full"/>
15740 <param name="separator" value=","/> 16404 <param name="separator" value=","/>
15750 <param name="adv_opts_selector" value="advanced"/> 16414 <param name="adv_opts_selector" value="advanced"/>
15751 <param name="force" value="false"/> 16415 <param name="force" value="false"/>
15752 <param name="test" value="true"/> 16416 <param name="test" value="true"/>
15753 </conditional> 16417 </conditional>
15754 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/> 16418 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
15755 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> 16419 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
15756 <param name="charge" value="1 2 3"/> 16420 <param name="charge" value="1 2 3"/>
15757 <param name="format" value="list"/> 16421 <param name="format" value="list"/>
15758 <param name="average_mass" value="false"/> 16422 <param name="average_mass" value="false"/>
15759 <param name="fragment_type" value="full"/> 16423 <param name="fragment_type" value="full"/>
15760 <param name="separator" value=""/> 16424 <param name="separator" value=""/>
15847 </assert_contents> 16511 </assert_contents>
15848 </output> 16512 </output>
15849 </test> 16513 </test>
15850 </xml> 16514 </xml>
15851 <xml name="autotest_MetaboliteAdductDecharger"> 16515 <xml name="autotest_MetaboliteAdductDecharger">
15852 </xml> 16516 <test expect_num_outputs="2">
16517 <conditional name="adv_opts_cond">
16518 <param name="adv_opts_selector" value="advanced"/>
16519 <param name="force" value="false"/>
16520 <param name="test" value="true"/>
16521 </conditional>
16522 <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
16523 <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16524 <section name="algorithm">
16525 <section name="MetaboliteFeatureDeconvolution">
16526 <param name="charge_min" value="1"/>
16527 <param name="charge_max" value="3"/>
16528 <param name="charge_span_max" value="3"/>
16529 <param name="q_try" value="feature"/>
16530 <param name="retention_max_diff" value="1.0"/>
16531 <param name="retention_max_diff_local" value="1.0"/>
16532 <param name="mass_max_diff" value="0.05"/>
16533 <param name="unit" value="Da"/>
16534 <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
16535 <param name="max_neutrals" value="1"/>
16536 <param name="use_minority_bound" value="true"/>
16537 <param name="max_minority_bound" value="3"/>
16538 <param name="min_rt_overlap" value="0.66"/>
16539 <param name="intensity_filter" value="false"/>
16540 <param name="negative_mode" value="false"/>
16541 <param name="default_map_label" value="decharged features"/>
16542 <param name="verbose_level" value="0"/>
16543 </section>
16544 </section>
16545 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
16546 <output name="ctd_out" ftype="xml">
16547 <assert_contents>
16548 <is_valid_xml/>
16549 </assert_contents>
16550 </output>
16551 </test>
16552 <test expect_num_outputs="3">
16553 <conditional name="adv_opts_cond">
16554 <param name="adv_opts_selector" value="advanced"/>
16555 <param name="force" value="false"/>
16556 <param name="test" value="true"/>
16557 </conditional>
16558 <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
16559 <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16560 <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16561 <section name="algorithm">
16562 <section name="MetaboliteFeatureDeconvolution">
16563 <param name="charge_min" value="1"/>
16564 <param name="charge_max" value="3"/>
16565 <param name="charge_span_max" value="3"/>
16566 <param name="q_try" value="feature"/>
16567 <param name="retention_max_diff" value="1.0"/>
16568 <param name="retention_max_diff_local" value="1.0"/>
16569 <param name="mass_max_diff" value="0.05"/>
16570 <param name="unit" value="Da"/>
16571 <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
16572 <param name="max_neutrals" value="1"/>
16573 <param name="use_minority_bound" value="true"/>
16574 <param name="max_minority_bound" value="3"/>
16575 <param name="min_rt_overlap" value="0.66"/>
16576 <param name="intensity_filter" value="false"/>
16577 <param name="negative_mode" value="false"/>
16578 <param name="default_map_label" value="decharged features"/>
16579 <param name="verbose_level" value="0"/>
16580 </section>
16581 </section>
16582 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
16583 <output name="ctd_out" ftype="xml">
16584 <assert_contents>
16585 <is_valid_xml/>
16586 </assert_contents>
16587 </output>
16588 </test>
16589 </xml>
15853 <xml name="autotest_MetaboliteSpectralMatcher"> 16590 <xml name="autotest_MetaboliteSpectralMatcher">
15854 </xml> 16591 </xml>
15855 <xml name="autotest_MetaProSIP"> 16592 <xml name="autotest_MetaProSIP">
15856 <test expect_num_outputs="3"> 16593 <test expect_num_outputs="3">
15857 <conditional name="adv_opts_cond"> 16594 <conditional name="adv_opts_cond">
16053 <xml name="autotest_MSFraggerAdapter"/> 16790 <xml name="autotest_MSFraggerAdapter"/>
16054 <xml name="autotest_MSGFPlusAdapter"> 16791 <xml name="autotest_MSGFPlusAdapter">
16055 <test expect_num_outputs="3"> 16792 <test expect_num_outputs="3">
16056 <conditional name="adv_opts_cond"> 16793 <conditional name="adv_opts_cond">
16057 <param name="adv_opts_selector" value="advanced"/> 16794 <param name="adv_opts_selector" value="advanced"/>
16795 <param name="add_decoys" value="false"/>
16058 <param name="legacy_conversion" value="false"/> 16796 <param name="legacy_conversion" value="false"/>
16059 <param name="force" value="false"/> 16797 <param name="force" value="false"/>
16060 <param name="test" value="true"/> 16798 <param name="test" value="true"/>
16061 </conditional> 16799 </conditional>
16062 <param name="in" value="spectra.mzML"/> 16800 <param name="in" value="spectra.mzML"/>
16063 <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 16801 <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16064 <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> 16802 <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
16065 <param name="database" value="proteins.fasta"/> 16803 <param name="database" value="proteins.fasta"/>
16066 <param name="add_decoys" value="false"/>
16067 <param name="precursor_mass_tolerance" value="10.0"/> 16804 <param name="precursor_mass_tolerance" value="10.0"/>
16068 <param name="precursor_error_units" value="ppm"/> 16805 <param name="precursor_error_units" value="ppm"/>
16069 <param name="isotope_error_range" value="0,1"/> 16806 <param name="isotope_error_range" value="0,1"/>
16070 <param name="fragment_method" value="from_spectrum"/> 16807 <param name="fragment_method" value="from_spectrum"/>
16071 <param name="instrument" value="high_res"/> 16808 <param name="instrument" value="high_res"/>
16077 <param name="min_peptide_length" value="6"/> 16814 <param name="min_peptide_length" value="6"/>
16078 <param name="max_peptide_length" value="40"/> 16815 <param name="max_peptide_length" value="40"/>
16079 <param name="matches_per_spec" value="1"/> 16816 <param name="matches_per_spec" value="1"/>
16080 <param name="add_features" value="false"/> 16817 <param name="add_features" value="false"/>
16081 <param name="max_mods" value="2"/> 16818 <param name="max_mods" value="2"/>
16819 <param name="max_missed_cleavages" value="-1"/>
16820 <param name="tasks" value="0"/>
16082 <param name="fixed_modifications" value=""/> 16821 <param name="fixed_modifications" value=""/>
16083 <param name="variable_modifications" value="Oxidation (M)"/> 16822 <param name="variable_modifications" value="Oxidation (M)"/>
16084 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> 16823 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
16085 <output name="ctd_out" ftype="xml"> 16824 <output name="ctd_out" ftype="xml">
16086 <assert_contents> 16825 <assert_contents>
16403 <param name="force" value="false"/> 17142 <param name="force" value="false"/>
16404 <param name="test" value="true"/> 17143 <param name="test" value="true"/>
16405 </conditional> 17144 </conditional>
16406 <param name="in" value="MzTabExporter_3_input.featureXML"/> 17145 <param name="in" value="MzTabExporter_3_input.featureXML"/>
16407 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> 17146 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17147 <param name="opt_columns" value="subfeatures"/>
17148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17149 <output name="ctd_out" ftype="xml">
17150 <assert_contents>
17151 <is_valid_xml/>
17152 </assert_contents>
17153 </output>
17154 </test>
17155 <test expect_num_outputs="2">
17156 <conditional name="adv_opts_cond">
17157 <param name="adv_opts_selector" value="advanced"/>
17158 <param name="first_run_inference_only" value="false"/>
17159 <param name="force" value="false"/>
17160 <param name="test" value="true"/>
17161 </conditional>
17162 <param name="in" value="Epifany_2_out.consensusXML"/>
17163 <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17164 <param name="opt_columns" value="subfeatures"/>
17165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17166 <output name="ctd_out" ftype="xml">
17167 <assert_contents>
17168 <is_valid_xml/>
17169 </assert_contents>
17170 </output>
17171 </test>
17172 <test expect_num_outputs="2">
17173 <conditional name="adv_opts_cond">
17174 <param name="adv_opts_selector" value="advanced"/>
17175 <param name="first_run_inference_only" value="true"/>
17176 <param name="force" value="false"/>
17177 <param name="test" value="true"/>
17178 </conditional>
17179 <param name="in" value="MzTabExporter_5_in.consensusXML"/>
17180 <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17181 <param name="opt_columns" value="subfeatures"/>
17182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17183 <output name="ctd_out" ftype="xml">
17184 <assert_contents>
17185 <is_valid_xml/>
17186 </assert_contents>
17187 </output>
17188 </test>
17189 <test expect_num_outputs="2">
17190 <conditional name="adv_opts_cond">
17191 <param name="adv_opts_selector" value="advanced"/>
17192 <param name="first_run_inference_only" value="false"/>
17193 <param name="force" value="false"/>
17194 <param name="test" value="true"/>
17195 </conditional>
17196 <param name="in" value="MzTabExporter_6_input.idXML"/>
17197 <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
17198 <param name="opt_columns" value="subfeatures"/>
17199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17200 <output name="ctd_out" ftype="xml">
17201 <assert_contents>
17202 <is_valid_xml/>
17203 </assert_contents>
17204 </output>
17205 </test>
17206 <test expect_num_outputs="2">
17207 <conditional name="adv_opts_cond">
17208 <param name="adv_opts_selector" value="advanced"/>
17209 <param name="first_run_inference_only" value="false"/>
17210 <param name="force" value="false"/>
17211 <param name="test" value="true"/>
17212 </conditional>
17213 <param name="in" value="MzTabExporter_7_input.consensusXML"/>
17214 <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
16408 <param name="opt_columns" value="subfeatures"/> 17215 <param name="opt_columns" value="subfeatures"/>
16409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 17216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16410 <output name="ctd_out" ftype="xml"> 17217 <output name="ctd_out" ftype="xml">
16411 <assert_contents> 17218 <assert_contents>
16412 <is_valid_xml/> 17219 <is_valid_xml/>
16917 <param name="spacing_for_spectra_resampling" value="0.005"/> 17724 <param name="spacing_for_spectra_resampling" value="0.005"/>
16918 <param name="uis_threshold_sn" value="-1"/> 17725 <param name="uis_threshold_sn" value="-1"/>
16919 <param name="uis_threshold_peak_area" value="0"/> 17726 <param name="uis_threshold_peak_area" value="0"/>
16920 <param name="scoring_model" value="default"/> 17727 <param name="scoring_model" value="default"/>
16921 <param name="im_extra_drift" value="0.0"/> 17728 <param name="im_extra_drift" value="0.0"/>
17729 <param name="strict" value="true"/>
16922 <section name="TransitionGroupPicker"> 17730 <section name="TransitionGroupPicker">
16923 <param name="stop_after_feature" value="-1"/> 17731 <param name="stop_after_feature" value="-1"/>
16924 <param name="stop_after_intensity_ratio" value="0.0001"/> 17732 <param name="stop_after_intensity_ratio" value="0.0001"/>
16925 <param name="min_peak_width" value="-1.0"/> 17733 <param name="min_peak_width" value="-1.0"/>
16926 <param name="peak_integration" value="original"/> 17734 <param name="peak_integration" value="original"/>
17028 <param name="spacing_for_spectra_resampling" value="0.005"/> 17836 <param name="spacing_for_spectra_resampling" value="0.005"/>
17029 <param name="uis_threshold_sn" value="-1"/> 17837 <param name="uis_threshold_sn" value="-1"/>
17030 <param name="uis_threshold_peak_area" value="0"/> 17838 <param name="uis_threshold_peak_area" value="0"/>
17031 <param name="scoring_model" value="default"/> 17839 <param name="scoring_model" value="default"/>
17032 <param name="im_extra_drift" value="0.0"/> 17840 <param name="im_extra_drift" value="0.0"/>
17841 <param name="strict" value="true"/>
17033 <section name="TransitionGroupPicker"> 17842 <section name="TransitionGroupPicker">
17034 <param name="stop_after_feature" value="-1"/> 17843 <param name="stop_after_feature" value="-1"/>
17035 <param name="stop_after_intensity_ratio" value="0.0001"/> 17844 <param name="stop_after_intensity_ratio" value="0.0001"/>
17036 <param name="min_peak_width" value="-1.0"/> 17845 <param name="min_peak_width" value="-1.0"/>
17037 <param name="peak_integration" value="original"/> 17846 <param name="peak_integration" value="original"/>
17139 <param name="spacing_for_spectra_resampling" value="0.005"/> 17948 <param name="spacing_for_spectra_resampling" value="0.005"/>
17140 <param name="uis_threshold_sn" value="-1"/> 17949 <param name="uis_threshold_sn" value="-1"/>
17141 <param name="uis_threshold_peak_area" value="0"/> 17950 <param name="uis_threshold_peak_area" value="0"/>
17142 <param name="scoring_model" value="default"/> 17951 <param name="scoring_model" value="default"/>
17143 <param name="im_extra_drift" value="0.0"/> 17952 <param name="im_extra_drift" value="0.0"/>
17953 <param name="strict" value="true"/>
17144 <section name="TransitionGroupPicker"> 17954 <section name="TransitionGroupPicker">
17145 <param name="stop_after_feature" value="-1"/> 17955 <param name="stop_after_feature" value="-1"/>
17146 <param name="stop_after_intensity_ratio" value="0.0001"/> 17956 <param name="stop_after_intensity_ratio" value="0.0001"/>
17147 <param name="min_peak_width" value="-1.0"/> 17957 <param name="min_peak_width" value="-1.0"/>
17148 <param name="peak_integration" value="original"/> 17958 <param name="peak_integration" value="original"/>
17250 <param name="spacing_for_spectra_resampling" value="0.005"/> 18060 <param name="spacing_for_spectra_resampling" value="0.005"/>
17251 <param name="uis_threshold_sn" value="-1"/> 18061 <param name="uis_threshold_sn" value="-1"/>
17252 <param name="uis_threshold_peak_area" value="0"/> 18062 <param name="uis_threshold_peak_area" value="0"/>
17253 <param name="scoring_model" value="default"/> 18063 <param name="scoring_model" value="default"/>
17254 <param name="im_extra_drift" value="0.0"/> 18064 <param name="im_extra_drift" value="0.0"/>
18065 <param name="strict" value="true"/>
17255 <section name="TransitionGroupPicker"> 18066 <section name="TransitionGroupPicker">
17256 <param name="stop_after_feature" value="-1"/> 18067 <param name="stop_after_feature" value="-1"/>
17257 <param name="stop_after_intensity_ratio" value="0.0001"/> 18068 <param name="stop_after_intensity_ratio" value="0.0001"/>
17258 <param name="min_peak_width" value="-1.0"/> 18069 <param name="min_peak_width" value="-1.0"/>
17259 <param name="peak_integration" value="original"/> 18070 <param name="peak_integration" value="original"/>
17360 <param name="spacing_for_spectra_resampling" value="0.005"/> 18171 <param name="spacing_for_spectra_resampling" value="0.005"/>
17361 <param name="uis_threshold_sn" value="-1"/> 18172 <param name="uis_threshold_sn" value="-1"/>
17362 <param name="uis_threshold_peak_area" value="0"/> 18173 <param name="uis_threshold_peak_area" value="0"/>
17363 <param name="scoring_model" value="default"/> 18174 <param name="scoring_model" value="default"/>
17364 <param name="im_extra_drift" value="0.0"/> 18175 <param name="im_extra_drift" value="0.0"/>
18176 <param name="strict" value="true"/>
17365 <section name="TransitionGroupPicker"> 18177 <section name="TransitionGroupPicker">
17366 <param name="stop_after_feature" value="-1"/> 18178 <param name="stop_after_feature" value="-1"/>
17367 <param name="stop_after_intensity_ratio" value="0.0001"/> 18179 <param name="stop_after_intensity_ratio" value="0.0001"/>
17368 <param name="min_peak_width" value="-1.0"/> 18180 <param name="min_peak_width" value="-1.0"/>
17369 <param name="peak_integration" value="original"/> 18181 <param name="peak_integration" value="original"/>
17471 <param name="spacing_for_spectra_resampling" value="0.005"/> 18283 <param name="spacing_for_spectra_resampling" value="0.005"/>
17472 <param name="uis_threshold_sn" value="-1"/> 18284 <param name="uis_threshold_sn" value="-1"/>
17473 <param name="uis_threshold_peak_area" value="0"/> 18285 <param name="uis_threshold_peak_area" value="0"/>
17474 <param name="scoring_model" value="default"/> 18286 <param name="scoring_model" value="default"/>
17475 <param name="im_extra_drift" value="0.0"/> 18287 <param name="im_extra_drift" value="0.0"/>
18288 <param name="strict" value="true"/>
17476 <section name="TransitionGroupPicker"> 18289 <section name="TransitionGroupPicker">
17477 <param name="stop_after_feature" value="-1"/> 18290 <param name="stop_after_feature" value="-1"/>
17478 <param name="stop_after_intensity_ratio" value="0.0001"/> 18291 <param name="stop_after_intensity_ratio" value="0.0001"/>
17479 <param name="min_peak_width" value="-1.0"/> 18292 <param name="min_peak_width" value="-1.0"/>
17480 <param name="peak_integration" value="original"/> 18293 <param name="peak_integration" value="original"/>
17582 <param name="spacing_for_spectra_resampling" value="0.005"/> 18395 <param name="spacing_for_spectra_resampling" value="0.005"/>
17583 <param name="uis_threshold_sn" value="-1"/> 18396 <param name="uis_threshold_sn" value="-1"/>
17584 <param name="uis_threshold_peak_area" value="0"/> 18397 <param name="uis_threshold_peak_area" value="0"/>
17585 <param name="scoring_model" value="default"/> 18398 <param name="scoring_model" value="default"/>
17586 <param name="im_extra_drift" value="0.0"/> 18399 <param name="im_extra_drift" value="0.0"/>
18400 <param name="strict" value="true"/>
17587 <section name="TransitionGroupPicker"> 18401 <section name="TransitionGroupPicker">
17588 <param name="stop_after_feature" value="-1"/> 18402 <param name="stop_after_feature" value="-1"/>
17589 <param name="stop_after_intensity_ratio" value="0.0001"/> 18403 <param name="stop_after_intensity_ratio" value="0.0001"/>
17590 <param name="min_peak_width" value="-1.0"/> 18404 <param name="min_peak_width" value="-1.0"/>
17591 <param name="peak_integration" value="original"/> 18405 <param name="peak_integration" value="original"/>
17693 <param name="spacing_for_spectra_resampling" value="0.005"/> 18507 <param name="spacing_for_spectra_resampling" value="0.005"/>
17694 <param name="uis_threshold_sn" value="-1"/> 18508 <param name="uis_threshold_sn" value="-1"/>
17695 <param name="uis_threshold_peak_area" value="0"/> 18509 <param name="uis_threshold_peak_area" value="0"/>
17696 <param name="scoring_model" value="default"/> 18510 <param name="scoring_model" value="default"/>
17697 <param name="im_extra_drift" value="0.0"/> 18511 <param name="im_extra_drift" value="0.0"/>
18512 <param name="strict" value="true"/>
17698 <section name="TransitionGroupPicker"> 18513 <section name="TransitionGroupPicker">
17699 <param name="stop_after_feature" value="-1"/> 18514 <param name="stop_after_feature" value="-1"/>
17700 <param name="stop_after_intensity_ratio" value="0.0001"/> 18515 <param name="stop_after_intensity_ratio" value="0.0001"/>
17701 <param name="min_peak_width" value="-1.0"/> 18516 <param name="min_peak_width" value="-1.0"/>
17702 <param name="peak_integration" value="original"/> 18517 <param name="peak_integration" value="original"/>
17804 <param name="spacing_for_spectra_resampling" value="0.005"/> 18619 <param name="spacing_for_spectra_resampling" value="0.005"/>
17805 <param name="uis_threshold_sn" value="-1"/> 18620 <param name="uis_threshold_sn" value="-1"/>
17806 <param name="uis_threshold_peak_area" value="0"/> 18621 <param name="uis_threshold_peak_area" value="0"/>
17807 <param name="scoring_model" value="default"/> 18622 <param name="scoring_model" value="default"/>
17808 <param name="im_extra_drift" value="0.0"/> 18623 <param name="im_extra_drift" value="0.0"/>
18624 <param name="strict" value="true"/>
17809 <section name="TransitionGroupPicker"> 18625 <section name="TransitionGroupPicker">
17810 <param name="stop_after_feature" value="-1"/> 18626 <param name="stop_after_feature" value="-1"/>
17811 <param name="stop_after_intensity_ratio" value="0.0001"/> 18627 <param name="stop_after_intensity_ratio" value="0.0001"/>
17812 <param name="min_peak_width" value="-1.0"/> 18628 <param name="min_peak_width" value="-1.0"/>
17813 <param name="peak_integration" value="original"/> 18629 <param name="peak_integration" value="original"/>
18288 <is_valid_xml/> 19104 <is_valid_xml/>
18289 </assert_contents> 19105 </assert_contents>
18290 </output> 19106 </output>
18291 </test> 19107 </test>
18292 </xml> 19108 </xml>
19109 <xml name="autotest_OpenSwathDIAPreScoring">
19110 </xml>
18293 <xml name="autotest_OpenSwathFeatureXMLToTSV"> 19111 <xml name="autotest_OpenSwathFeatureXMLToTSV">
18294 <test expect_num_outputs="2"> 19112 <test expect_num_outputs="2">
18295 <conditional name="adv_opts_cond"> 19113 <conditional name="adv_opts_cond">
18296 <param name="adv_opts_selector" value="advanced"/> 19114 <param name="adv_opts_selector" value="advanced"/>
18297 <param name="force" value="false"/> 19115 <param name="force" value="false"/>
18592 <param name="spacing_for_spectra_resampling" value="0.005"/> 19410 <param name="spacing_for_spectra_resampling" value="0.005"/>
18593 <param name="uis_threshold_sn" value="-1"/> 19411 <param name="uis_threshold_sn" value="-1"/>
18594 <param name="uis_threshold_peak_area" value="0"/> 19412 <param name="uis_threshold_peak_area" value="0"/>
18595 <param name="scoring_model" value="default"/> 19413 <param name="scoring_model" value="default"/>
18596 <param name="im_extra_drift" value="0.0"/> 19414 <param name="im_extra_drift" value="0.0"/>
19415 <param name="strict" value="true"/>
18597 <section name="TransitionGroupPicker"> 19416 <section name="TransitionGroupPicker">
18598 <param name="stop_after_feature" value="-1"/> 19417 <param name="stop_after_feature" value="-1"/>
18599 <param name="stop_after_intensity_ratio" value="0.0001"/> 19418 <param name="stop_after_intensity_ratio" value="0.0001"/>
18600 <param name="min_peak_width" value="-1.0"/> 19419 <param name="min_peak_width" value="-1.0"/>
18601 <param name="peak_integration" value="original"/> 19420 <param name="peak_integration" value="original"/>
18713 <param name="spacing_for_spectra_resampling" value="0.005"/> 19532 <param name="spacing_for_spectra_resampling" value="0.005"/>
18714 <param name="uis_threshold_sn" value="-1"/> 19533 <param name="uis_threshold_sn" value="-1"/>
18715 <param name="uis_threshold_peak_area" value="0"/> 19534 <param name="uis_threshold_peak_area" value="0"/>
18716 <param name="scoring_model" value="default"/> 19535 <param name="scoring_model" value="default"/>
18717 <param name="im_extra_drift" value="0.0"/> 19536 <param name="im_extra_drift" value="0.0"/>
19537 <param name="strict" value="true"/>
18718 <section name="TransitionGroupPicker"> 19538 <section name="TransitionGroupPicker">
18719 <param name="stop_after_feature" value="-1"/> 19539 <param name="stop_after_feature" value="-1"/>
18720 <param name="stop_after_intensity_ratio" value="0.0001"/> 19540 <param name="stop_after_intensity_ratio" value="0.0001"/>
18721 <param name="min_peak_width" value="-1.0"/> 19541 <param name="min_peak_width" value="-1.0"/>
18722 <param name="peak_integration" value="original"/> 19542 <param name="peak_integration" value="original"/>
18834 <param name="spacing_for_spectra_resampling" value="0.005"/> 19654 <param name="spacing_for_spectra_resampling" value="0.005"/>
18835 <param name="uis_threshold_sn" value="-1"/> 19655 <param name="uis_threshold_sn" value="-1"/>
18836 <param name="uis_threshold_peak_area" value="0"/> 19656 <param name="uis_threshold_peak_area" value="0"/>
18837 <param name="scoring_model" value="default"/> 19657 <param name="scoring_model" value="default"/>
18838 <param name="im_extra_drift" value="0.0"/> 19658 <param name="im_extra_drift" value="0.0"/>
19659 <param name="strict" value="true"/>
18839 <section name="TransitionGroupPicker"> 19660 <section name="TransitionGroupPicker">
18840 <param name="stop_after_feature" value="-1"/> 19661 <param name="stop_after_feature" value="-1"/>
18841 <param name="stop_after_intensity_ratio" value="0.0001"/> 19662 <param name="stop_after_intensity_ratio" value="0.0001"/>
18842 <param name="min_peak_width" value="-1.0"/> 19663 <param name="min_peak_width" value="-1.0"/>
18843 <param name="peak_integration" value="original"/> 19664 <param name="peak_integration" value="original"/>
18930 <test expect_num_outputs="4"> 19751 <test expect_num_outputs="4">
18931 <conditional name="adv_opts_cond"> 19752 <conditional name="adv_opts_cond">
18932 <param name="adv_opts_selector" value="advanced"/> 19753 <param name="adv_opts_selector" value="advanced"/>
18933 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> 19754 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
18934 <param name="sort_swath_maps" value="false"/> 19755 <param name="sort_swath_maps" value="false"/>
18935 <param name="use_ms1_traces" value="false"/> 19756 <param name="enable_ms1" value="false"/>
18936 <param name="enable_uis_scoring" value="false"/> 19757 <param name="enable_ipf" value="true"/>
18937 <param name="out_chrom_type" value="mzML"/> 19758 <param name="out_chrom_type" value="mzML"/>
18938 <param name="min_upper_edge_dist" value="0.0"/> 19759 <param name="min_upper_edge_dist" value="0.0"/>
18939 <param name="extra_rt_extraction_window" value="0.0"/> 19760 <param name="extra_rt_extraction_window" value="0.0"/>
18940 <param name="mz_extraction_window_unit" value="Th"/> 19761 <param name="mz_extraction_window_unit" value="ppm"/>
18941 <param name="mz_extraction_window_ms1_unit" value="Th"/> 19762 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
18942 <param name="use_ms1_ion_mobility" value="true"/> 19763 <param name="use_ms1_ion_mobility" value="true"/>
18943 <param name="matching_window_only" value="false"/> 19764 <param name="matching_window_only" value="false"/>
18944 <param name="irt_mz_extraction_window" value="0.05"/> 19765 <param name="irt_mz_extraction_window" value="50.0"/>
18945 <param name="irt_mz_extraction_window_unit" value="Th"/> 19766 <param name="irt_mz_extraction_window_unit" value="ppm"/>
18946 <param name="irt_im_extraction_window" value="-1.0"/> 19767 <param name="irt_im_extraction_window" value="-1.0"/>
18947 <param name="min_rsq" value="0.95"/> 19768 <param name="min_rsq" value="0.95"/>
18948 <param name="min_coverage" value="0.6"/> 19769 <param name="min_coverage" value="0.6"/>
18949 <param name="split_file_input" value="false"/> 19770 <param name="split_file_input" value="false"/>
18950 <param name="use_elution_model_score" value="false"/> 19771 <param name="use_elution_model_score" value="false"/>
18951 <param name="readOptions" value="normal"/> 19772 <param name="readOptions" value="normal"/>
18952 <param name="mz_correction_function" value="none"/> 19773 <param name="mz_correction_function" value="none"/>
18953 <param name="extraction_function" value="tophat"/> 19774 <param name="extraction_function" value="tophat"/>
18954 <param name="batchSize" value="250"/> 19775 <param name="batchSize" value="1000"/>
18955 <param name="ms1_isotopes" value="0"/> 19776 <param name="ms1_isotopes" value="3"/>
18956 <param name="force" value="false"/> 19777 <param name="force" value="false"/>
18957 <param name="test" value="true"/> 19778 <param name="test" value="false"/>
18958 </conditional> 19779 </conditional>
18959 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> 19780 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
18960 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 19781 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
18961 <param name="tr_type" value=""/> 19782 <param name="tr_type" value=""/>
18962 <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> 19783 <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18963 <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 19784 <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18964 <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> 19785 <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
18965 <param name="sonar" value="false"/> 19786 <param name="sonar" value="false"/>
18966 <param name="rt_extraction_window" value="600.0"/> 19787 <param name="rt_extraction_window" value="600.0"/>
18967 <param name="ion_mobility_window" value="-1.0"/> 19788 <param name="ion_mobility_window" value="-1.0"/>
18968 <param name="mz_extraction_window" value="0.05"/> 19789 <param name="mz_extraction_window" value="50.0"/>
18969 <param name="mz_extraction_window_ms1" value="0.05"/> 19790 <param name="mz_extraction_window_ms1" value="50.0"/>
18970 <param name="im_extraction_window_ms1" value="-1.0"/> 19791 <param name="im_extraction_window_ms1" value="-1.0"/>
18971 <section name="Debugging"/> 19792 <section name="Debugging"/>
18972 <section name="Calibration"> 19793 <section name="Calibration">
18973 <param name="ms1_im_calibration" value="false"/> 19794 <param name="ms1_im_calibration" value="false"/>
18974 <param name="im_correction_function" value="linear"/> 19795 <param name="im_correction_function" value="linear"/>
18992 <param name="OverallQualityCutoff" value="5.5"/> 19813 <param name="OverallQualityCutoff" value="5.5"/>
18993 <param name="NrRTBins" value="10"/> 19814 <param name="NrRTBins" value="10"/>
18994 <param name="MinPeptidesPerBin" value="1"/> 19815 <param name="MinPeptidesPerBin" value="1"/>
18995 <param name="MinBinsFilled" value="8"/> 19816 <param name="MinBinsFilled" value="8"/>
18996 <section name="lowess"> 19817 <section name="lowess">
18997 <param name="span" value="0.666666666666667"/> 19818 <param name="span" value="0.05"/>
18998 </section> 19819 </section>
18999 <section name="b_spline"> 19820 <section name="b_spline">
19000 <param name="num_nodes" value="5"/> 19821 <param name="num_nodes" value="5"/>
19001 </section> 19822 </section>
19002 </section> 19823 </section>
19006 <param name="quantification_cutoff" value="0.0"/> 19827 <param name="quantification_cutoff" value="0.0"/>
19007 <param name="write_convex_hull" value="false"/> 19828 <param name="write_convex_hull" value="false"/>
19008 <param name="spectrum_addition_method" value="simple"/> 19829 <param name="spectrum_addition_method" value="simple"/>
19009 <param name="add_up_spectra" value="1"/> 19830 <param name="add_up_spectra" value="1"/>
19010 <param name="spacing_for_spectra_resampling" value="0.005"/> 19831 <param name="spacing_for_spectra_resampling" value="0.005"/>
19011 <param name="uis_threshold_sn" value="0"/> 19832 <param name="uis_threshold_sn" value="-1"/>
19012 <param name="uis_threshold_peak_area" value="0"/> 19833 <param name="uis_threshold_peak_area" value="0"/>
19013 <param name="scoring_model" value="default"/> 19834 <param name="scoring_model" value="default"/>
19014 <param name="im_extra_drift" value="0.0"/> 19835 <param name="im_extra_drift" value="0.0"/>
19836 <param name="strict" value="true"/>
19837 <section name="TransitionGroupPicker">
19838 <param name="stop_after_feature" value="-1"/>
19839 <param name="min_peak_width" value="-1.0"/>
19840 <param name="peak_integration" value="original"/>
19841 <param name="background_subtraction" value="none"/>
19842 <param name="recalculate_peaks" value="true"/>
19843 <param name="use_precursors" value="false"/>
19844 <param name="use_consensus" value="true"/>
19845 <param name="recalculate_peaks_max_z" value="0.75"/>
19846 <param name="minimal_quality" value="-1.5"/>
19847 <param name="resample_boundary" value="15.0"/>
19848 <param name="compute_peak_quality" value="false"/>
19849 <param name="compute_peak_shape_metrics" value="false"/>
19850 <param name="compute_total_mi" value="false"/>
19851 <param name="boundary_selection_method" value="largest"/>
19852 <section name="PeakPickerMRM">
19853 <param name="sgolay_frame_length" value="11"/>
19854 <param name="sgolay_polynomial_order" value="3"/>
19855 <param name="gauss_width" value="30.0"/>
19856 <param name="use_gauss" value="false"/>
19857 <param name="peak_width" value="-1.0"/>
19858 <param name="signal_to_noise" value="0.1"/>
19859 <param name="write_sn_log_messages" value="false"/>
19860 <param name="remove_overlapping_peaks" value="true"/>
19861 <param name="method" value="corrected"/>
19862 </section>
19863 <section name="PeakIntegrator">
19864 <param name="integration_type" value="intensity_sum"/>
19865 <param name="baseline_type" value="base_to_base"/>
19866 <param name="fit_EMG" value="false"/>
19867 </section>
19868 </section>
19869 <section name="DIAScoring">
19870 <param name="dia_extraction_window" value="0.05"/>
19871 <param name="dia_extraction_unit" value="Th"/>
19872 <param name="dia_centroided" value="false"/>
19873 <param name="dia_byseries_intensity_min" value="300.0"/>
19874 <param name="dia_byseries_ppm_diff" value="10.0"/>
19875 <param name="dia_nr_isotopes" value="4"/>
19876 <param name="dia_nr_charges" value="4"/>
19877 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19878 </section>
19879 <section name="EMGScoring">
19880 <param name="max_iteration" value="10"/>
19881 </section>
19882 <section name="Scores">
19883 <param name="use_shape_score" value="true"/>
19884 <param name="use_coelution_score" value="true"/>
19885 <param name="use_rt_score" value="true"/>
19886 <param name="use_library_score" value="true"/>
19887 <param name="use_intensity_score" value="true"/>
19888 <param name="use_nr_peaks_score" value="true"/>
19889 <param name="use_total_xic_score" value="true"/>
19890 <param name="use_total_mi_score" value="false"/>
19891 <param name="use_sn_score" value="true"/>
19892 <param name="use_mi_score" value="true"/>
19893 <param name="use_dia_scores" value="true"/>
19894 <param name="use_ms1_correlation" value="false"/>
19895 <param name="use_sonar_scores" value="false"/>
19896 <param name="use_ion_mobility_scores" value="false"/>
19897 <param name="use_ms1_fullscan" value="false"/>
19898 <param name="use_ms1_mi" value="true"/>
19899 <param name="use_uis_scores" value="false"/>
19900 </section>
19901 </section>
19902 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
19903 <output name="ctd_out" ftype="xml">
19904 <assert_contents>
19905 <is_valid_xml/>
19906 </assert_contents>
19907 </output>
19908 </test>
19909 <test expect_num_outputs="3">
19910 <conditional name="adv_opts_cond">
19911 <param name="adv_opts_selector" value="advanced"/>
19912 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
19913 <param name="sort_swath_maps" value="false"/>
19914 <param name="enable_ms1" value="false"/>
19915 <param name="enable_ipf" value="true"/>
19916 <param name="out_chrom_type" value="mzML"/>
19917 <param name="min_upper_edge_dist" value="0.0"/>
19918 <param name="extra_rt_extraction_window" value="0.0"/>
19919 <param name="mz_extraction_window_unit" value="ppm"/>
19920 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19921 <param name="use_ms1_ion_mobility" value="true"/>
19922 <param name="matching_window_only" value="false"/>
19923 <param name="irt_mz_extraction_window" value="50.0"/>
19924 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19925 <param name="irt_im_extraction_window" value="-1.0"/>
19926 <param name="min_rsq" value="0.95"/>
19927 <param name="min_coverage" value="0.6"/>
19928 <param name="split_file_input" value="false"/>
19929 <param name="use_elution_model_score" value="false"/>
19930 <param name="readOptions" value="normal"/>
19931 <param name="mz_correction_function" value="none"/>
19932 <param name="extraction_function" value="tophat"/>
19933 <param name="batchSize" value="1000"/>
19934 <param name="ms1_isotopes" value="3"/>
19935 <param name="force" value="false"/>
19936 <param name="test" value="false"/>
19937 </conditional>
19938 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
19939 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
19940 <param name="tr_type" value=""/>
19941 <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19942 <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19943 <param name="sonar" value="false"/>
19944 <param name="rt_extraction_window" value="600.0"/>
19945 <param name="ion_mobility_window" value="-1.0"/>
19946 <param name="mz_extraction_window" value="50.0"/>
19947 <param name="mz_extraction_window_ms1" value="50.0"/>
19948 <param name="im_extraction_window_ms1" value="-1.0"/>
19949 <section name="Debugging"/>
19950 <section name="Calibration">
19951 <param name="ms1_im_calibration" value="false"/>
19952 <param name="im_correction_function" value="linear"/>
19953 <param name="debug_im_file" value=""/>
19954 <param name="debug_mz_file" value=""/>
19955 </section>
19956 <section name="Library">
19957 <param name="retentionTimeInterpretation" value="iRT"/>
19958 <param name="override_group_label_check" value="false"/>
19959 <param name="force_invalid_mods" value="false"/>
19960 </section>
19961 <section name="RTNormalization">
19962 <param name="alignmentMethod" value="linear"/>
19963 <param name="outlierMethod" value="iter_residual"/>
19964 <param name="useIterativeChauvenet" value="false"/>
19965 <param name="RANSACMaxIterations" value="1000"/>
19966 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19967 <param name="RANSACSamplingSize" value="10"/>
19968 <param name="estimateBestPeptides" value="false"/>
19969 <param name="InitialQualityCutoff" value="0.5"/>
19970 <param name="OverallQualityCutoff" value="5.5"/>
19971 <param name="NrRTBins" value="10"/>
19972 <param name="MinPeptidesPerBin" value="1"/>
19973 <param name="MinBinsFilled" value="8"/>
19974 <section name="lowess">
19975 <param name="span" value="0.05"/>
19976 </section>
19977 <section name="b_spline">
19978 <param name="num_nodes" value="5"/>
19979 </section>
19980 </section>
19981 <section name="Scoring">
19982 <param name="stop_report_after_feature" value="5"/>
19983 <param name="rt_normalization_factor" value="100.0"/>
19984 <param name="quantification_cutoff" value="0.0"/>
19985 <param name="write_convex_hull" value="false"/>
19986 <param name="spectrum_addition_method" value="simple"/>
19987 <param name="add_up_spectra" value="1"/>
19988 <param name="spacing_for_spectra_resampling" value="0.005"/>
19989 <param name="uis_threshold_sn" value="-1"/>
19990 <param name="uis_threshold_peak_area" value="0"/>
19991 <param name="scoring_model" value="default"/>
19992 <param name="im_extra_drift" value="0.0"/>
19993 <param name="strict" value="true"/>
19994 <section name="TransitionGroupPicker">
19995 <param name="stop_after_feature" value="-1"/>
19996 <param name="min_peak_width" value="-1.0"/>
19997 <param name="peak_integration" value="original"/>
19998 <param name="background_subtraction" value="none"/>
19999 <param name="recalculate_peaks" value="true"/>
20000 <param name="use_precursors" value="false"/>
20001 <param name="use_consensus" value="true"/>
20002 <param name="recalculate_peaks_max_z" value="0.75"/>
20003 <param name="minimal_quality" value="-1.5"/>
20004 <param name="resample_boundary" value="15.0"/>
20005 <param name="compute_peak_quality" value="false"/>
20006 <param name="compute_peak_shape_metrics" value="false"/>
20007 <param name="compute_total_mi" value="false"/>
20008 <param name="boundary_selection_method" value="largest"/>
20009 <section name="PeakPickerMRM">
20010 <param name="sgolay_frame_length" value="11"/>
20011 <param name="sgolay_polynomial_order" value="3"/>
20012 <param name="gauss_width" value="30.0"/>
20013 <param name="use_gauss" value="false"/>
20014 <param name="peak_width" value="-1.0"/>
20015 <param name="signal_to_noise" value="0.1"/>
20016 <param name="write_sn_log_messages" value="false"/>
20017 <param name="remove_overlapping_peaks" value="true"/>
20018 <param name="method" value="corrected"/>
20019 </section>
20020 <section name="PeakIntegrator">
20021 <param name="integration_type" value="intensity_sum"/>
20022 <param name="baseline_type" value="base_to_base"/>
20023 <param name="fit_EMG" value="false"/>
20024 </section>
20025 </section>
20026 <section name="DIAScoring">
20027 <param name="dia_extraction_window" value="0.05"/>
20028 <param name="dia_extraction_unit" value="Th"/>
20029 <param name="dia_centroided" value="false"/>
20030 <param name="dia_byseries_intensity_min" value="300.0"/>
20031 <param name="dia_byseries_ppm_diff" value="10.0"/>
20032 <param name="dia_nr_isotopes" value="4"/>
20033 <param name="dia_nr_charges" value="4"/>
20034 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20035 </section>
20036 <section name="EMGScoring">
20037 <param name="max_iteration" value="10"/>
20038 </section>
20039 <section name="Scores">
20040 <param name="use_shape_score" value="true"/>
20041 <param name="use_coelution_score" value="true"/>
20042 <param name="use_rt_score" value="true"/>
20043 <param name="use_library_score" value="true"/>
20044 <param name="use_intensity_score" value="true"/>
20045 <param name="use_nr_peaks_score" value="true"/>
20046 <param name="use_total_xic_score" value="true"/>
20047 <param name="use_total_mi_score" value="false"/>
20048 <param name="use_sn_score" value="true"/>
20049 <param name="use_mi_score" value="true"/>
20050 <param name="use_dia_scores" value="true"/>
20051 <param name="use_ms1_correlation" value="false"/>
20052 <param name="use_sonar_scores" value="false"/>
20053 <param name="use_ion_mobility_scores" value="false"/>
20054 <param name="use_ms1_fullscan" value="false"/>
20055 <param name="use_ms1_mi" value="true"/>
20056 <param name="use_uis_scores" value="false"/>
20057 </section>
20058 </section>
20059 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20060 <output name="ctd_out" ftype="xml">
20061 <assert_contents>
20062 <is_valid_xml/>
20063 </assert_contents>
20064 </output>
20065 </test>
20066 <test expect_num_outputs="3">
20067 <conditional name="adv_opts_cond">
20068 <param name="adv_opts_selector" value="advanced"/>
20069 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20070 <param name="sort_swath_maps" value="false"/>
20071 <param name="enable_ms1" value="true"/>
20072 <param name="enable_ipf" value="true"/>
20073 <param name="out_chrom_type" value="mzML"/>
20074 <param name="min_upper_edge_dist" value="0.0"/>
20075 <param name="extra_rt_extraction_window" value="0.0"/>
20076 <param name="mz_extraction_window_unit" value="ppm"/>
20077 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20078 <param name="use_ms1_ion_mobility" value="true"/>
20079 <param name="matching_window_only" value="false"/>
20080 <param name="irt_mz_extraction_window" value="50.0"/>
20081 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20082 <param name="irt_im_extraction_window" value="-1.0"/>
20083 <param name="min_rsq" value="0.95"/>
20084 <param name="min_coverage" value="0.6"/>
20085 <param name="split_file_input" value="false"/>
20086 <param name="use_elution_model_score" value="false"/>
20087 <param name="readOptions" value="normal"/>
20088 <param name="mz_correction_function" value="none"/>
20089 <param name="extraction_function" value="tophat"/>
20090 <param name="batchSize" value="1000"/>
20091 <param name="ms1_isotopes" value="3"/>
20092 <param name="force" value="false"/>
20093 <param name="test" value="false"/>
20094 </conditional>
20095 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20096 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20097 <param name="tr_type" value=""/>
20098 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20099 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20100 <param name="sonar" value="false"/>
20101 <param name="rt_extraction_window" value="600.0"/>
20102 <param name="ion_mobility_window" value="-1.0"/>
20103 <param name="mz_extraction_window" value="50.0"/>
20104 <param name="mz_extraction_window_ms1" value="50.0"/>
20105 <param name="im_extraction_window_ms1" value="-1.0"/>
20106 <section name="Debugging"/>
20107 <section name="Calibration">
20108 <param name="ms1_im_calibration" value="false"/>
20109 <param name="im_correction_function" value="linear"/>
20110 <param name="debug_im_file" value=""/>
20111 <param name="debug_mz_file" value=""/>
20112 </section>
20113 <section name="Library">
20114 <param name="retentionTimeInterpretation" value="iRT"/>
20115 <param name="override_group_label_check" value="false"/>
20116 <param name="force_invalid_mods" value="false"/>
20117 </section>
20118 <section name="RTNormalization">
20119 <param name="alignmentMethod" value="linear"/>
20120 <param name="outlierMethod" value="iter_residual"/>
20121 <param name="useIterativeChauvenet" value="false"/>
20122 <param name="RANSACMaxIterations" value="1000"/>
20123 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20124 <param name="RANSACSamplingSize" value="10"/>
20125 <param name="estimateBestPeptides" value="false"/>
20126 <param name="InitialQualityCutoff" value="0.5"/>
20127 <param name="OverallQualityCutoff" value="5.5"/>
20128 <param name="NrRTBins" value="10"/>
20129 <param name="MinPeptidesPerBin" value="1"/>
20130 <param name="MinBinsFilled" value="8"/>
20131 <section name="lowess">
20132 <param name="span" value="0.05"/>
20133 </section>
20134 <section name="b_spline">
20135 <param name="num_nodes" value="5"/>
20136 </section>
20137 </section>
20138 <section name="Scoring">
20139 <param name="stop_report_after_feature" value="5"/>
20140 <param name="rt_normalization_factor" value="100.0"/>
20141 <param name="quantification_cutoff" value="0.0"/>
20142 <param name="write_convex_hull" value="false"/>
20143 <param name="spectrum_addition_method" value="simple"/>
20144 <param name="add_up_spectra" value="1"/>
20145 <param name="spacing_for_spectra_resampling" value="0.005"/>
20146 <param name="uis_threshold_sn" value="-1"/>
20147 <param name="uis_threshold_peak_area" value="0"/>
20148 <param name="scoring_model" value="default"/>
20149 <param name="im_extra_drift" value="0.0"/>
20150 <param name="strict" value="true"/>
20151 <section name="TransitionGroupPicker">
20152 <param name="stop_after_feature" value="-1"/>
20153 <param name="min_peak_width" value="-1.0"/>
20154 <param name="peak_integration" value="original"/>
20155 <param name="background_subtraction" value="none"/>
20156 <param name="recalculate_peaks" value="true"/>
20157 <param name="use_precursors" value="false"/>
20158 <param name="use_consensus" value="true"/>
20159 <param name="recalculate_peaks_max_z" value="0.75"/>
20160 <param name="minimal_quality" value="-1.5"/>
20161 <param name="resample_boundary" value="15.0"/>
20162 <param name="compute_peak_quality" value="false"/>
20163 <param name="compute_peak_shape_metrics" value="false"/>
20164 <param name="compute_total_mi" value="false"/>
20165 <param name="boundary_selection_method" value="largest"/>
20166 <section name="PeakPickerMRM">
20167 <param name="sgolay_frame_length" value="11"/>
20168 <param name="sgolay_polynomial_order" value="3"/>
20169 <param name="gauss_width" value="30.0"/>
20170 <param name="use_gauss" value="false"/>
20171 <param name="peak_width" value="-1.0"/>
20172 <param name="signal_to_noise" value="0.1"/>
20173 <param name="write_sn_log_messages" value="false"/>
20174 <param name="remove_overlapping_peaks" value="true"/>
20175 <param name="method" value="corrected"/>
20176 </section>
20177 <section name="PeakIntegrator">
20178 <param name="integration_type" value="intensity_sum"/>
20179 <param name="baseline_type" value="base_to_base"/>
20180 <param name="fit_EMG" value="false"/>
20181 </section>
20182 </section>
20183 <section name="DIAScoring">
20184 <param name="dia_extraction_window" value="0.05"/>
20185 <param name="dia_extraction_unit" value="Th"/>
20186 <param name="dia_centroided" value="false"/>
20187 <param name="dia_byseries_intensity_min" value="300.0"/>
20188 <param name="dia_byseries_ppm_diff" value="10.0"/>
20189 <param name="dia_nr_isotopes" value="4"/>
20190 <param name="dia_nr_charges" value="4"/>
20191 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20192 </section>
20193 <section name="EMGScoring">
20194 <param name="max_iteration" value="10"/>
20195 </section>
20196 <section name="Scores">
20197 <param name="use_shape_score" value="true"/>
20198 <param name="use_coelution_score" value="true"/>
20199 <param name="use_rt_score" value="true"/>
20200 <param name="use_library_score" value="true"/>
20201 <param name="use_intensity_score" value="true"/>
20202 <param name="use_nr_peaks_score" value="true"/>
20203 <param name="use_total_xic_score" value="true"/>
20204 <param name="use_total_mi_score" value="false"/>
20205 <param name="use_sn_score" value="true"/>
20206 <param name="use_mi_score" value="true"/>
20207 <param name="use_dia_scores" value="true"/>
20208 <param name="use_ms1_correlation" value="false"/>
20209 <param name="use_sonar_scores" value="false"/>
20210 <param name="use_ion_mobility_scores" value="false"/>
20211 <param name="use_ms1_fullscan" value="false"/>
20212 <param name="use_ms1_mi" value="true"/>
20213 <param name="use_uis_scores" value="false"/>
20214 </section>
20215 </section>
20216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20217 <output name="ctd_out" ftype="xml">
20218 <assert_contents>
20219 <is_valid_xml/>
20220 </assert_contents>
20221 </output>
20222 </test>
20223 <test expect_num_outputs="3">
20224 <conditional name="adv_opts_cond">
20225 <param name="adv_opts_selector" value="advanced"/>
20226 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20227 <param name="sort_swath_maps" value="false"/>
20228 <param name="enable_ms1" value="true"/>
20229 <param name="enable_ipf" value="true"/>
20230 <param name="out_chrom_type" value="mzML"/>
20231 <param name="min_upper_edge_dist" value="0.0"/>
20232 <param name="extra_rt_extraction_window" value="0.0"/>
20233 <param name="mz_extraction_window_unit" value="ppm"/>
20234 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20235 <param name="use_ms1_ion_mobility" value="true"/>
20236 <param name="matching_window_only" value="false"/>
20237 <param name="irt_mz_extraction_window" value="50.0"/>
20238 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20239 <param name="irt_im_extraction_window" value="-1.0"/>
20240 <param name="min_rsq" value="0.95"/>
20241 <param name="min_coverage" value="0.6"/>
20242 <param name="split_file_input" value="false"/>
20243 <param name="use_elution_model_score" value="false"/>
20244 <param name="readOptions" value="normal"/>
20245 <param name="mz_correction_function" value="none"/>
20246 <param name="extraction_function" value="tophat"/>
20247 <param name="batchSize" value="1000"/>
20248 <param name="ms1_isotopes" value="3"/>
20249 <param name="force" value="false"/>
20250 <param name="test" value="false"/>
20251 </conditional>
20252 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20253 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20254 <param name="tr_type" value=""/>
20255 <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
20256 <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20257 <param name="sonar" value="false"/>
20258 <param name="rt_extraction_window" value="600.0"/>
20259 <param name="ion_mobility_window" value="-1.0"/>
20260 <param name="mz_extraction_window" value="50.0"/>
20261 <param name="mz_extraction_window_ms1" value="50.0"/>
20262 <param name="im_extraction_window_ms1" value="-1.0"/>
20263 <section name="Debugging"/>
20264 <section name="Calibration">
20265 <param name="ms1_im_calibration" value="false"/>
20266 <param name="im_correction_function" value="linear"/>
20267 <param name="debug_im_file" value=""/>
20268 <param name="debug_mz_file" value=""/>
20269 </section>
20270 <section name="Library">
20271 <param name="retentionTimeInterpretation" value="iRT"/>
20272 <param name="override_group_label_check" value="false"/>
20273 <param name="force_invalid_mods" value="false"/>
20274 </section>
20275 <section name="RTNormalization">
20276 <param name="alignmentMethod" value="linear"/>
20277 <param name="outlierMethod" value="iter_residual"/>
20278 <param name="useIterativeChauvenet" value="false"/>
20279 <param name="RANSACMaxIterations" value="1000"/>
20280 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20281 <param name="RANSACSamplingSize" value="10"/>
20282 <param name="estimateBestPeptides" value="false"/>
20283 <param name="InitialQualityCutoff" value="0.5"/>
20284 <param name="OverallQualityCutoff" value="5.5"/>
20285 <param name="NrRTBins" value="10"/>
20286 <param name="MinPeptidesPerBin" value="1"/>
20287 <param name="MinBinsFilled" value="8"/>
20288 <section name="lowess">
20289 <param name="span" value="0.05"/>
20290 </section>
20291 <section name="b_spline">
20292 <param name="num_nodes" value="5"/>
20293 </section>
20294 </section>
20295 <section name="Scoring">
20296 <param name="stop_report_after_feature" value="5"/>
20297 <param name="rt_normalization_factor" value="100.0"/>
20298 <param name="quantification_cutoff" value="0.0"/>
20299 <param name="write_convex_hull" value="false"/>
20300 <param name="spectrum_addition_method" value="simple"/>
20301 <param name="add_up_spectra" value="1"/>
20302 <param name="spacing_for_spectra_resampling" value="0.005"/>
20303 <param name="uis_threshold_sn" value="-1"/>
20304 <param name="uis_threshold_peak_area" value="0"/>
20305 <param name="scoring_model" value="default"/>
20306 <param name="im_extra_drift" value="0.0"/>
20307 <param name="strict" value="true"/>
20308 <section name="TransitionGroupPicker">
20309 <param name="stop_after_feature" value="-1"/>
20310 <param name="min_peak_width" value="-1.0"/>
20311 <param name="peak_integration" value="original"/>
20312 <param name="background_subtraction" value="none"/>
20313 <param name="recalculate_peaks" value="true"/>
20314 <param name="use_precursors" value="false"/>
20315 <param name="use_consensus" value="true"/>
20316 <param name="recalculate_peaks_max_z" value="0.75"/>
20317 <param name="minimal_quality" value="-1.5"/>
20318 <param name="resample_boundary" value="15.0"/>
20319 <param name="compute_peak_quality" value="false"/>
20320 <param name="compute_peak_shape_metrics" value="false"/>
20321 <param name="compute_total_mi" value="false"/>
20322 <param name="boundary_selection_method" value="largest"/>
20323 <section name="PeakPickerMRM">
20324 <param name="sgolay_frame_length" value="11"/>
20325 <param name="sgolay_polynomial_order" value="3"/>
20326 <param name="gauss_width" value="30.0"/>
20327 <param name="use_gauss" value="false"/>
20328 <param name="peak_width" value="-1.0"/>
20329 <param name="signal_to_noise" value="0.1"/>
20330 <param name="write_sn_log_messages" value="false"/>
20331 <param name="remove_overlapping_peaks" value="true"/>
20332 <param name="method" value="corrected"/>
20333 </section>
20334 <section name="PeakIntegrator">
20335 <param name="integration_type" value="intensity_sum"/>
20336 <param name="baseline_type" value="base_to_base"/>
20337 <param name="fit_EMG" value="false"/>
20338 </section>
20339 </section>
20340 <section name="DIAScoring">
20341 <param name="dia_extraction_window" value="0.05"/>
20342 <param name="dia_extraction_unit" value="Th"/>
20343 <param name="dia_centroided" value="false"/>
20344 <param name="dia_byseries_intensity_min" value="300.0"/>
20345 <param name="dia_byseries_ppm_diff" value="10.0"/>
20346 <param name="dia_nr_isotopes" value="4"/>
20347 <param name="dia_nr_charges" value="4"/>
20348 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20349 </section>
20350 <section name="EMGScoring">
20351 <param name="max_iteration" value="10"/>
20352 </section>
20353 <section name="Scores">
20354 <param name="use_shape_score" value="true"/>
20355 <param name="use_coelution_score" value="true"/>
20356 <param name="use_rt_score" value="true"/>
20357 <param name="use_library_score" value="true"/>
20358 <param name="use_intensity_score" value="true"/>
20359 <param name="use_nr_peaks_score" value="true"/>
20360 <param name="use_total_xic_score" value="true"/>
20361 <param name="use_total_mi_score" value="false"/>
20362 <param name="use_sn_score" value="true"/>
20363 <param name="use_mi_score" value="true"/>
20364 <param name="use_dia_scores" value="true"/>
20365 <param name="use_ms1_correlation" value="false"/>
20366 <param name="use_sonar_scores" value="false"/>
20367 <param name="use_ion_mobility_scores" value="false"/>
20368 <param name="use_ms1_fullscan" value="false"/>
20369 <param name="use_ms1_mi" value="true"/>
20370 <param name="use_uis_scores" value="false"/>
20371 </section>
20372 </section>
20373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
20374 <output name="ctd_out" ftype="xml">
20375 <assert_contents>
20376 <is_valid_xml/>
20377 </assert_contents>
20378 </output>
20379 </test>
20380 <test expect_num_outputs="3">
20381 <conditional name="adv_opts_cond">
20382 <param name="adv_opts_selector" value="advanced"/>
20383 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20384 <param name="sort_swath_maps" value="false"/>
20385 <param name="enable_ms1" value="true"/>
20386 <param name="enable_ipf" value="true"/>
20387 <param name="out_chrom_type" value="mzML"/>
20388 <param name="min_upper_edge_dist" value="0.0"/>
20389 <param name="extra_rt_extraction_window" value="0.0"/>
20390 <param name="mz_extraction_window_unit" value="ppm"/>
20391 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20392 <param name="use_ms1_ion_mobility" value="true"/>
20393 <param name="matching_window_only" value="false"/>
20394 <param name="irt_mz_extraction_window" value="50.0"/>
20395 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20396 <param name="irt_im_extraction_window" value="-1.0"/>
20397 <param name="min_rsq" value="0.95"/>
20398 <param name="min_coverage" value="0.6"/>
20399 <param name="split_file_input" value="false"/>
20400 <param name="use_elution_model_score" value="false"/>
20401 <param name="readOptions" value="cache"/>
20402 <param name="mz_correction_function" value="none"/>
20403 <param name="extraction_function" value="tophat"/>
20404 <param name="batchSize" value="1000"/>
20405 <param name="ms1_isotopes" value="3"/>
20406 <param name="force" value="false"/>
20407 <param name="test" value="false"/>
20408 </conditional>
20409 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20410 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20411 <param name="tr_type" value=""/>
20412 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20413 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20414 <param name="sonar" value="false"/>
20415 <param name="rt_extraction_window" value="600.0"/>
20416 <param name="ion_mobility_window" value="-1.0"/>
20417 <param name="mz_extraction_window" value="50.0"/>
20418 <param name="mz_extraction_window_ms1" value="50.0"/>
20419 <param name="im_extraction_window_ms1" value="-1.0"/>
20420 <section name="Debugging"/>
20421 <section name="Calibration">
20422 <param name="ms1_im_calibration" value="false"/>
20423 <param name="im_correction_function" value="linear"/>
20424 <param name="debug_im_file" value=""/>
20425 <param name="debug_mz_file" value=""/>
20426 </section>
20427 <section name="Library">
20428 <param name="retentionTimeInterpretation" value="iRT"/>
20429 <param name="override_group_label_check" value="false"/>
20430 <param name="force_invalid_mods" value="false"/>
20431 </section>
20432 <section name="RTNormalization">
20433 <param name="alignmentMethod" value="linear"/>
20434 <param name="outlierMethod" value="iter_residual"/>
20435 <param name="useIterativeChauvenet" value="false"/>
20436 <param name="RANSACMaxIterations" value="1000"/>
20437 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20438 <param name="RANSACSamplingSize" value="10"/>
20439 <param name="estimateBestPeptides" value="false"/>
20440 <param name="InitialQualityCutoff" value="0.5"/>
20441 <param name="OverallQualityCutoff" value="5.5"/>
20442 <param name="NrRTBins" value="10"/>
20443 <param name="MinPeptidesPerBin" value="1"/>
20444 <param name="MinBinsFilled" value="8"/>
20445 <section name="lowess">
20446 <param name="span" value="0.05"/>
20447 </section>
20448 <section name="b_spline">
20449 <param name="num_nodes" value="5"/>
20450 </section>
20451 </section>
20452 <section name="Scoring">
20453 <param name="stop_report_after_feature" value="5"/>
20454 <param name="rt_normalization_factor" value="100.0"/>
20455 <param name="quantification_cutoff" value="0.0"/>
20456 <param name="write_convex_hull" value="false"/>
20457 <param name="spectrum_addition_method" value="simple"/>
20458 <param name="add_up_spectra" value="1"/>
20459 <param name="spacing_for_spectra_resampling" value="0.005"/>
20460 <param name="uis_threshold_sn" value="-1"/>
20461 <param name="uis_threshold_peak_area" value="0"/>
20462 <param name="scoring_model" value="default"/>
20463 <param name="im_extra_drift" value="0.0"/>
20464 <param name="strict" value="true"/>
20465 <section name="TransitionGroupPicker">
20466 <param name="stop_after_feature" value="-1"/>
20467 <param name="min_peak_width" value="-1.0"/>
20468 <param name="peak_integration" value="original"/>
20469 <param name="background_subtraction" value="none"/>
20470 <param name="recalculate_peaks" value="true"/>
20471 <param name="use_precursors" value="false"/>
20472 <param name="use_consensus" value="true"/>
20473 <param name="recalculate_peaks_max_z" value="0.75"/>
20474 <param name="minimal_quality" value="-1.5"/>
20475 <param name="resample_boundary" value="15.0"/>
20476 <param name="compute_peak_quality" value="false"/>
20477 <param name="compute_peak_shape_metrics" value="false"/>
20478 <param name="compute_total_mi" value="false"/>
20479 <param name="boundary_selection_method" value="largest"/>
20480 <section name="PeakPickerMRM">
20481 <param name="sgolay_frame_length" value="11"/>
20482 <param name="sgolay_polynomial_order" value="3"/>
20483 <param name="gauss_width" value="30.0"/>
20484 <param name="use_gauss" value="false"/>
20485 <param name="peak_width" value="-1.0"/>
20486 <param name="signal_to_noise" value="0.1"/>
20487 <param name="write_sn_log_messages" value="false"/>
20488 <param name="remove_overlapping_peaks" value="true"/>
20489 <param name="method" value="corrected"/>
20490 </section>
20491 <section name="PeakIntegrator">
20492 <param name="integration_type" value="intensity_sum"/>
20493 <param name="baseline_type" value="base_to_base"/>
20494 <param name="fit_EMG" value="false"/>
20495 </section>
20496 </section>
20497 <section name="DIAScoring">
20498 <param name="dia_extraction_window" value="0.05"/>
20499 <param name="dia_extraction_unit" value="Th"/>
20500 <param name="dia_centroided" value="false"/>
20501 <param name="dia_byseries_intensity_min" value="300.0"/>
20502 <param name="dia_byseries_ppm_diff" value="10.0"/>
20503 <param name="dia_nr_isotopes" value="4"/>
20504 <param name="dia_nr_charges" value="4"/>
20505 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20506 </section>
20507 <section name="EMGScoring">
20508 <param name="max_iteration" value="10"/>
20509 </section>
20510 <section name="Scores">
20511 <param name="use_shape_score" value="true"/>
20512 <param name="use_coelution_score" value="true"/>
20513 <param name="use_rt_score" value="true"/>
20514 <param name="use_library_score" value="true"/>
20515 <param name="use_intensity_score" value="true"/>
20516 <param name="use_nr_peaks_score" value="true"/>
20517 <param name="use_total_xic_score" value="true"/>
20518 <param name="use_total_mi_score" value="false"/>
20519 <param name="use_sn_score" value="true"/>
20520 <param name="use_mi_score" value="true"/>
20521 <param name="use_dia_scores" value="true"/>
20522 <param name="use_ms1_correlation" value="false"/>
20523 <param name="use_sonar_scores" value="false"/>
20524 <param name="use_ion_mobility_scores" value="false"/>
20525 <param name="use_ms1_fullscan" value="false"/>
20526 <param name="use_ms1_mi" value="true"/>
20527 <param name="use_uis_scores" value="false"/>
20528 </section>
20529 </section>
20530 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20531 <output name="ctd_out" ftype="xml">
20532 <assert_contents>
20533 <is_valid_xml/>
20534 </assert_contents>
20535 </output>
20536 </test>
20537 <test expect_num_outputs="3">
20538 <conditional name="adv_opts_cond">
20539 <param name="adv_opts_selector" value="advanced"/>
20540 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20541 <param name="sort_swath_maps" value="false"/>
20542 <param name="enable_ms1" value="true"/>
20543 <param name="enable_ipf" value="true"/>
20544 <param name="out_chrom_type" value="mzML"/>
20545 <param name="min_upper_edge_dist" value="0.0"/>
20546 <param name="extra_rt_extraction_window" value="0.0"/>
20547 <param name="mz_extraction_window_unit" value="ppm"/>
20548 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20549 <param name="use_ms1_ion_mobility" value="true"/>
20550 <param name="matching_window_only" value="false"/>
20551 <param name="irt_mz_extraction_window" value="50.0"/>
20552 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20553 <param name="irt_im_extraction_window" value="-1.0"/>
20554 <param name="min_rsq" value="0.95"/>
20555 <param name="min_coverage" value="0.6"/>
20556 <param name="split_file_input" value="false"/>
20557 <param name="use_elution_model_score" value="false"/>
20558 <param name="readOptions" value="cacheWorkingInMemory"/>
20559 <param name="mz_correction_function" value="none"/>
20560 <param name="extraction_function" value="tophat"/>
20561 <param name="batchSize" value="1000"/>
20562 <param name="ms1_isotopes" value="3"/>
20563 <param name="force" value="false"/>
20564 <param name="test" value="false"/>
20565 </conditional>
20566 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20567 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20568 <param name="tr_type" value=""/>
20569 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20570 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20571 <param name="sonar" value="false"/>
20572 <param name="rt_extraction_window" value="600.0"/>
20573 <param name="ion_mobility_window" value="-1.0"/>
20574 <param name="mz_extraction_window" value="50.0"/>
20575 <param name="mz_extraction_window_ms1" value="50.0"/>
20576 <param name="im_extraction_window_ms1" value="-1.0"/>
20577 <section name="Debugging"/>
20578 <section name="Calibration">
20579 <param name="ms1_im_calibration" value="false"/>
20580 <param name="im_correction_function" value="linear"/>
20581 <param name="debug_im_file" value=""/>
20582 <param name="debug_mz_file" value=""/>
20583 </section>
20584 <section name="Library">
20585 <param name="retentionTimeInterpretation" value="iRT"/>
20586 <param name="override_group_label_check" value="false"/>
20587 <param name="force_invalid_mods" value="false"/>
20588 </section>
20589 <section name="RTNormalization">
20590 <param name="alignmentMethod" value="linear"/>
20591 <param name="outlierMethod" value="iter_residual"/>
20592 <param name="useIterativeChauvenet" value="false"/>
20593 <param name="RANSACMaxIterations" value="1000"/>
20594 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20595 <param name="RANSACSamplingSize" value="10"/>
20596 <param name="estimateBestPeptides" value="false"/>
20597 <param name="InitialQualityCutoff" value="0.5"/>
20598 <param name="OverallQualityCutoff" value="5.5"/>
20599 <param name="NrRTBins" value="10"/>
20600 <param name="MinPeptidesPerBin" value="1"/>
20601 <param name="MinBinsFilled" value="8"/>
20602 <section name="lowess">
20603 <param name="span" value="0.05"/>
20604 </section>
20605 <section name="b_spline">
20606 <param name="num_nodes" value="5"/>
20607 </section>
20608 </section>
20609 <section name="Scoring">
20610 <param name="stop_report_after_feature" value="5"/>
20611 <param name="rt_normalization_factor" value="100.0"/>
20612 <param name="quantification_cutoff" value="0.0"/>
20613 <param name="write_convex_hull" value="false"/>
20614 <param name="spectrum_addition_method" value="simple"/>
20615 <param name="add_up_spectra" value="1"/>
20616 <param name="spacing_for_spectra_resampling" value="0.005"/>
20617 <param name="uis_threshold_sn" value="-1"/>
20618 <param name="uis_threshold_peak_area" value="0"/>
20619 <param name="scoring_model" value="default"/>
20620 <param name="im_extra_drift" value="0.0"/>
20621 <param name="strict" value="true"/>
20622 <section name="TransitionGroupPicker">
20623 <param name="stop_after_feature" value="-1"/>
20624 <param name="min_peak_width" value="-1.0"/>
20625 <param name="peak_integration" value="original"/>
20626 <param name="background_subtraction" value="none"/>
20627 <param name="recalculate_peaks" value="true"/>
20628 <param name="use_precursors" value="false"/>
20629 <param name="use_consensus" value="true"/>
20630 <param name="recalculate_peaks_max_z" value="0.75"/>
20631 <param name="minimal_quality" value="-1.5"/>
20632 <param name="resample_boundary" value="15.0"/>
20633 <param name="compute_peak_quality" value="false"/>
20634 <param name="compute_peak_shape_metrics" value="false"/>
20635 <param name="compute_total_mi" value="false"/>
20636 <param name="boundary_selection_method" value="largest"/>
20637 <section name="PeakPickerMRM">
20638 <param name="sgolay_frame_length" value="11"/>
20639 <param name="sgolay_polynomial_order" value="3"/>
20640 <param name="gauss_width" value="30.0"/>
20641 <param name="use_gauss" value="false"/>
20642 <param name="peak_width" value="-1.0"/>
20643 <param name="signal_to_noise" value="0.1"/>
20644 <param name="write_sn_log_messages" value="false"/>
20645 <param name="remove_overlapping_peaks" value="true"/>
20646 <param name="method" value="corrected"/>
20647 </section>
20648 <section name="PeakIntegrator">
20649 <param name="integration_type" value="intensity_sum"/>
20650 <param name="baseline_type" value="base_to_base"/>
20651 <param name="fit_EMG" value="false"/>
20652 </section>
20653 </section>
20654 <section name="DIAScoring">
20655 <param name="dia_extraction_window" value="0.05"/>
20656 <param name="dia_extraction_unit" value="Th"/>
20657 <param name="dia_centroided" value="false"/>
20658 <param name="dia_byseries_intensity_min" value="300.0"/>
20659 <param name="dia_byseries_ppm_diff" value="10.0"/>
20660 <param name="dia_nr_isotopes" value="4"/>
20661 <param name="dia_nr_charges" value="4"/>
20662 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20663 </section>
20664 <section name="EMGScoring">
20665 <param name="max_iteration" value="10"/>
20666 </section>
20667 <section name="Scores">
20668 <param name="use_shape_score" value="true"/>
20669 <param name="use_coelution_score" value="true"/>
20670 <param name="use_rt_score" value="true"/>
20671 <param name="use_library_score" value="true"/>
20672 <param name="use_intensity_score" value="true"/>
20673 <param name="use_nr_peaks_score" value="true"/>
20674 <param name="use_total_xic_score" value="true"/>
20675 <param name="use_total_mi_score" value="false"/>
20676 <param name="use_sn_score" value="true"/>
20677 <param name="use_mi_score" value="true"/>
20678 <param name="use_dia_scores" value="true"/>
20679 <param name="use_ms1_correlation" value="false"/>
20680 <param name="use_sonar_scores" value="false"/>
20681 <param name="use_ion_mobility_scores" value="false"/>
20682 <param name="use_ms1_fullscan" value="false"/>
20683 <param name="use_ms1_mi" value="true"/>
20684 <param name="use_uis_scores" value="false"/>
20685 </section>
20686 </section>
20687 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20688 <output name="ctd_out" ftype="xml">
20689 <assert_contents>
20690 <is_valid_xml/>
20691 </assert_contents>
20692 </output>
20693 </test>
20694 <test expect_num_outputs="3">
20695 <conditional name="adv_opts_cond">
20696 <param name="adv_opts_selector" value="advanced"/>
20697 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20698 <param name="sort_swath_maps" value="false"/>
20699 <param name="enable_ms1" value="true"/>
20700 <param name="enable_ipf" value="true"/>
20701 <param name="out_chrom_type" value="mzML"/>
20702 <param name="min_upper_edge_dist" value="0.0"/>
20703 <param name="extra_rt_extraction_window" value="0.0"/>
20704 <param name="mz_extraction_window_unit" value="ppm"/>
20705 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20706 <param name="use_ms1_ion_mobility" value="true"/>
20707 <param name="matching_window_only" value="false"/>
20708 <param name="irt_mz_extraction_window" value="50.0"/>
20709 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20710 <param name="irt_im_extraction_window" value="-1.0"/>
20711 <param name="min_rsq" value="0.95"/>
20712 <param name="min_coverage" value="0.6"/>
20713 <param name="split_file_input" value="false"/>
20714 <param name="use_elution_model_score" value="false"/>
20715 <param name="readOptions" value="normal"/>
20716 <param name="mz_correction_function" value="none"/>
20717 <param name="extraction_function" value="tophat"/>
20718 <param name="batchSize" value="1000"/>
20719 <param name="ms1_isotopes" value="3"/>
20720 <param name="force" value="false"/>
20721 <param name="test" value="false"/>
20722 </conditional>
20723 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20724 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20725 <param name="tr_type" value=""/>
20726 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
20727 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20728 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20729 <param name="sonar" value="false"/>
20730 <param name="rt_extraction_window" value="600.0"/>
20731 <param name="ion_mobility_window" value="-1.0"/>
20732 <param name="mz_extraction_window" value="50.0"/>
20733 <param name="mz_extraction_window_ms1" value="50.0"/>
20734 <param name="im_extraction_window_ms1" value="-1.0"/>
20735 <section name="Debugging"/>
20736 <section name="Calibration">
20737 <param name="ms1_im_calibration" value="false"/>
20738 <param name="im_correction_function" value="linear"/>
20739 <param name="debug_im_file" value=""/>
20740 <param name="debug_mz_file" value=""/>
20741 </section>
20742 <section name="Library">
20743 <param name="retentionTimeInterpretation" value="iRT"/>
20744 <param name="override_group_label_check" value="false"/>
20745 <param name="force_invalid_mods" value="false"/>
20746 </section>
20747 <section name="RTNormalization">
20748 <param name="alignmentMethod" value="linear"/>
20749 <param name="outlierMethod" value="iter_residual"/>
20750 <param name="useIterativeChauvenet" value="false"/>
20751 <param name="RANSACMaxIterations" value="1000"/>
20752 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20753 <param name="RANSACSamplingSize" value="10"/>
20754 <param name="estimateBestPeptides" value="false"/>
20755 <param name="InitialQualityCutoff" value="0.5"/>
20756 <param name="OverallQualityCutoff" value="5.5"/>
20757 <param name="NrRTBins" value="10"/>
20758 <param name="MinPeptidesPerBin" value="1"/>
20759 <param name="MinBinsFilled" value="8"/>
20760 <section name="lowess">
20761 <param name="span" value="0.05"/>
20762 </section>
20763 <section name="b_spline">
20764 <param name="num_nodes" value="5"/>
20765 </section>
20766 </section>
20767 <section name="Scoring">
20768 <param name="stop_report_after_feature" value="5"/>
20769 <param name="rt_normalization_factor" value="100.0"/>
20770 <param name="quantification_cutoff" value="0.0"/>
20771 <param name="write_convex_hull" value="false"/>
20772 <param name="spectrum_addition_method" value="simple"/>
20773 <param name="add_up_spectra" value="1"/>
20774 <param name="spacing_for_spectra_resampling" value="0.005"/>
20775 <param name="uis_threshold_sn" value="-1"/>
20776 <param name="uis_threshold_peak_area" value="0"/>
20777 <param name="scoring_model" value="default"/>
20778 <param name="im_extra_drift" value="0.0"/>
20779 <param name="strict" value="true"/>
20780 <section name="TransitionGroupPicker">
20781 <param name="stop_after_feature" value="-1"/>
20782 <param name="min_peak_width" value="-1.0"/>
20783 <param name="peak_integration" value="original"/>
20784 <param name="background_subtraction" value="none"/>
20785 <param name="recalculate_peaks" value="true"/>
20786 <param name="use_precursors" value="false"/>
20787 <param name="use_consensus" value="true"/>
20788 <param name="recalculate_peaks_max_z" value="0.75"/>
20789 <param name="minimal_quality" value="-1.5"/>
20790 <param name="resample_boundary" value="15.0"/>
20791 <param name="compute_peak_quality" value="false"/>
20792 <param name="compute_peak_shape_metrics" value="false"/>
20793 <param name="compute_total_mi" value="false"/>
20794 <param name="boundary_selection_method" value="largest"/>
20795 <section name="PeakPickerMRM">
20796 <param name="sgolay_frame_length" value="11"/>
20797 <param name="sgolay_polynomial_order" value="3"/>
20798 <param name="gauss_width" value="30.0"/>
20799 <param name="use_gauss" value="false"/>
20800 <param name="peak_width" value="-1.0"/>
20801 <param name="signal_to_noise" value="0.1"/>
20802 <param name="write_sn_log_messages" value="false"/>
20803 <param name="remove_overlapping_peaks" value="true"/>
20804 <param name="method" value="corrected"/>
20805 </section>
20806 <section name="PeakIntegrator">
20807 <param name="integration_type" value="intensity_sum"/>
20808 <param name="baseline_type" value="base_to_base"/>
20809 <param name="fit_EMG" value="false"/>
20810 </section>
20811 </section>
20812 <section name="DIAScoring">
20813 <param name="dia_extraction_window" value="0.05"/>
20814 <param name="dia_extraction_unit" value="Th"/>
20815 <param name="dia_centroided" value="false"/>
20816 <param name="dia_byseries_intensity_min" value="300.0"/>
20817 <param name="dia_byseries_ppm_diff" value="10.0"/>
20818 <param name="dia_nr_isotopes" value="4"/>
20819 <param name="dia_nr_charges" value="4"/>
20820 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20821 </section>
20822 <section name="EMGScoring">
20823 <param name="max_iteration" value="10"/>
20824 </section>
20825 <section name="Scores">
20826 <param name="use_shape_score" value="true"/>
20827 <param name="use_coelution_score" value="true"/>
20828 <param name="use_rt_score" value="true"/>
20829 <param name="use_library_score" value="true"/>
20830 <param name="use_intensity_score" value="true"/>
20831 <param name="use_nr_peaks_score" value="true"/>
20832 <param name="use_total_xic_score" value="true"/>
20833 <param name="use_total_mi_score" value="false"/>
20834 <param name="use_sn_score" value="true"/>
20835 <param name="use_mi_score" value="true"/>
20836 <param name="use_dia_scores" value="true"/>
20837 <param name="use_ms1_correlation" value="false"/>
20838 <param name="use_sonar_scores" value="false"/>
20839 <param name="use_ion_mobility_scores" value="false"/>
20840 <param name="use_ms1_fullscan" value="false"/>
20841 <param name="use_ms1_mi" value="true"/>
20842 <param name="use_uis_scores" value="false"/>
20843 </section>
20844 </section>
20845 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20846 <output name="ctd_out" ftype="xml">
20847 <assert_contents>
20848 <is_valid_xml/>
20849 </assert_contents>
20850 </output>
20851 </test>
20852 <test expect_num_outputs="3">
20853 <conditional name="adv_opts_cond">
20854 <param name="adv_opts_selector" value="advanced"/>
20855 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20856 <param name="sort_swath_maps" value="false"/>
20857 <param name="enable_ms1" value="true"/>
20858 <param name="enable_ipf" value="true"/>
20859 <param name="out_chrom_type" value="mzML"/>
20860 <param name="min_upper_edge_dist" value="0.0"/>
20861 <param name="extra_rt_extraction_window" value="0.0"/>
20862 <param name="mz_extraction_window_unit" value="ppm"/>
20863 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
20864 <param name="use_ms1_ion_mobility" value="true"/>
20865 <param name="matching_window_only" value="false"/>
20866 <param name="irt_mz_extraction_window" value="50.0"/>
20867 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20868 <param name="irt_im_extraction_window" value="-1.0"/>
20869 <param name="min_rsq" value="0.95"/>
20870 <param name="min_coverage" value="0.6"/>
20871 <param name="split_file_input" value="false"/>
20872 <param name="use_elution_model_score" value="false"/>
20873 <param name="readOptions" value="normal"/>
20874 <param name="mz_correction_function" value="none"/>
20875 <param name="extraction_function" value="tophat"/>
20876 <param name="batchSize" value="1000"/>
20877 <param name="ms1_isotopes" value="3"/>
20878 <param name="force" value="true"/>
20879 <param name="test" value="false"/>
20880 </conditional>
20881 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20882 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20883 <param name="tr_type" value=""/>
20884 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
20885 <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20886 <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20887 <param name="sonar" value="false"/>
20888 <param name="rt_extraction_window" value="600.0"/>
20889 <param name="ion_mobility_window" value="-1.0"/>
20890 <param name="mz_extraction_window" value="50.0"/>
20891 <param name="mz_extraction_window_ms1" value="50.0"/>
20892 <param name="im_extraction_window_ms1" value="-1.0"/>
20893 <section name="Debugging"/>
20894 <section name="Calibration">
20895 <param name="ms1_im_calibration" value="false"/>
20896 <param name="im_correction_function" value="linear"/>
20897 <param name="debug_im_file" value=""/>
20898 <param name="debug_mz_file" value=""/>
20899 </section>
20900 <section name="Library">
20901 <param name="retentionTimeInterpretation" value="iRT"/>
20902 <param name="override_group_label_check" value="false"/>
20903 <param name="force_invalid_mods" value="false"/>
20904 </section>
20905 <section name="RTNormalization">
20906 <param name="alignmentMethod" value="linear"/>
20907 <param name="outlierMethod" value="iter_residual"/>
20908 <param name="useIterativeChauvenet" value="false"/>
20909 <param name="RANSACMaxIterations" value="1000"/>
20910 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20911 <param name="RANSACSamplingSize" value="10"/>
20912 <param name="estimateBestPeptides" value="false"/>
20913 <param name="InitialQualityCutoff" value="0.5"/>
20914 <param name="OverallQualityCutoff" value="5.5"/>
20915 <param name="NrRTBins" value="10"/>
20916 <param name="MinPeptidesPerBin" value="1"/>
20917 <param name="MinBinsFilled" value="8"/>
20918 <section name="lowess">
20919 <param name="span" value="0.05"/>
20920 </section>
20921 <section name="b_spline">
20922 <param name="num_nodes" value="5"/>
20923 </section>
20924 </section>
20925 <section name="Scoring">
20926 <param name="stop_report_after_feature" value="5"/>
20927 <param name="rt_normalization_factor" value="100.0"/>
20928 <param name="quantification_cutoff" value="0.0"/>
20929 <param name="write_convex_hull" value="false"/>
20930 <param name="spectrum_addition_method" value="simple"/>
20931 <param name="add_up_spectra" value="1"/>
20932 <param name="spacing_for_spectra_resampling" value="0.005"/>
20933 <param name="uis_threshold_sn" value="-1"/>
20934 <param name="uis_threshold_peak_area" value="0"/>
20935 <param name="scoring_model" value="default"/>
20936 <param name="im_extra_drift" value="0.0"/>
20937 <param name="strict" value="true"/>
20938 <section name="TransitionGroupPicker">
20939 <param name="stop_after_feature" value="-1"/>
20940 <param name="min_peak_width" value="-1.0"/>
20941 <param name="peak_integration" value="original"/>
20942 <param name="background_subtraction" value="none"/>
20943 <param name="recalculate_peaks" value="true"/>
20944 <param name="use_precursors" value="false"/>
20945 <param name="use_consensus" value="true"/>
20946 <param name="recalculate_peaks_max_z" value="0.75"/>
20947 <param name="minimal_quality" value="-1.5"/>
20948 <param name="resample_boundary" value="15.0"/>
20949 <param name="compute_peak_quality" value="false"/>
20950 <param name="compute_peak_shape_metrics" value="false"/>
20951 <param name="compute_total_mi" value="false"/>
20952 <param name="boundary_selection_method" value="largest"/>
20953 <section name="PeakPickerMRM">
20954 <param name="sgolay_frame_length" value="11"/>
20955 <param name="sgolay_polynomial_order" value="3"/>
20956 <param name="gauss_width" value="30.0"/>
20957 <param name="use_gauss" value="false"/>
20958 <param name="peak_width" value="-1.0"/>
20959 <param name="signal_to_noise" value="0.1"/>
20960 <param name="write_sn_log_messages" value="false"/>
20961 <param name="remove_overlapping_peaks" value="true"/>
20962 <param name="method" value="corrected"/>
20963 </section>
20964 <section name="PeakIntegrator">
20965 <param name="integration_type" value="intensity_sum"/>
20966 <param name="baseline_type" value="base_to_base"/>
20967 <param name="fit_EMG" value="false"/>
20968 </section>
20969 </section>
20970 <section name="DIAScoring">
20971 <param name="dia_extraction_window" value="0.05"/>
20972 <param name="dia_extraction_unit" value="Th"/>
20973 <param name="dia_centroided" value="false"/>
20974 <param name="dia_byseries_intensity_min" value="300.0"/>
20975 <param name="dia_byseries_ppm_diff" value="10.0"/>
20976 <param name="dia_nr_isotopes" value="4"/>
20977 <param name="dia_nr_charges" value="4"/>
20978 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20979 </section>
20980 <section name="EMGScoring">
20981 <param name="max_iteration" value="10"/>
20982 </section>
20983 <section name="Scores">
20984 <param name="use_shape_score" value="true"/>
20985 <param name="use_coelution_score" value="true"/>
20986 <param name="use_rt_score" value="true"/>
20987 <param name="use_library_score" value="true"/>
20988 <param name="use_intensity_score" value="true"/>
20989 <param name="use_nr_peaks_score" value="true"/>
20990 <param name="use_total_xic_score" value="true"/>
20991 <param name="use_total_mi_score" value="false"/>
20992 <param name="use_sn_score" value="true"/>
20993 <param name="use_mi_score" value="true"/>
20994 <param name="use_dia_scores" value="true"/>
20995 <param name="use_ms1_correlation" value="false"/>
20996 <param name="use_sonar_scores" value="false"/>
20997 <param name="use_ion_mobility_scores" value="false"/>
20998 <param name="use_ms1_fullscan" value="false"/>
20999 <param name="use_ms1_mi" value="true"/>
21000 <param name="use_uis_scores" value="false"/>
21001 </section>
21002 </section>
21003 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21004 <output name="ctd_out" ftype="xml">
21005 <assert_contents>
21006 <is_valid_xml/>
21007 </assert_contents>
21008 </output>
21009 </test>
21010 <test expect_num_outputs="3">
21011 <conditional name="adv_opts_cond">
21012 <param name="adv_opts_selector" value="advanced"/>
21013 <param name="sort_swath_maps" value="false"/>
21014 <param name="enable_ms1" value="false"/>
21015 <param name="enable_ipf" value="true"/>
21016 <param name="out_chrom_type" value="mzML"/>
21017 <param name="min_upper_edge_dist" value="0.0"/>
21018 <param name="extra_rt_extraction_window" value="0.0"/>
21019 <param name="mz_extraction_window_unit" value="ppm"/>
21020 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21021 <param name="use_ms1_ion_mobility" value="true"/>
21022 <param name="matching_window_only" value="false"/>
21023 <param name="irt_mz_extraction_window" value="550.0"/>
21024 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21025 <param name="irt_im_extraction_window" value="-1.0"/>
21026 <param name="min_rsq" value="0.95"/>
21027 <param name="min_coverage" value="0.6"/>
21028 <param name="split_file_input" value="false"/>
21029 <param name="use_elution_model_score" value="false"/>
21030 <param name="readOptions" value="normal"/>
21031 <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
21032 <param name="extraction_function" value="tophat"/>
21033 <param name="batchSize" value="1000"/>
21034 <param name="ms1_isotopes" value="3"/>
21035 <param name="force" value="false"/>
21036 <param name="test" value="false"/>
21037 </conditional>
21038 <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
21039 <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
21040 <param name="tr_type" value=""/>
21041 <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
21042 <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21043 <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21044 <param name="sonar" value="true"/>
21045 <param name="rt_extraction_window" value="-1.0"/>
21046 <param name="ion_mobility_window" value="-1.0"/>
21047 <param name="mz_extraction_window" value="0.2"/>
21048 <param name="mz_extraction_window_ms1" value="50.0"/>
21049 <param name="im_extraction_window_ms1" value="-1.0"/>
21050 <section name="Debugging"/>
21051 <section name="Calibration">
21052 <param name="ms1_im_calibration" value="false"/>
21053 <param name="im_correction_function" value="linear"/>
21054 <param name="debug_im_file" value=""/>
21055 <param name="debug_mz_file" value=""/>
21056 </section>
21057 <section name="Library">
21058 <param name="retentionTimeInterpretation" value="iRT"/>
21059 <param name="override_group_label_check" value="false"/>
21060 <param name="force_invalid_mods" value="false"/>
21061 </section>
21062 <section name="RTNormalization">
21063 <param name="alignmentMethod" value="linear"/>
21064 <param name="outlierMethod" value="none"/>
21065 <param name="useIterativeChauvenet" value="false"/>
21066 <param name="RANSACMaxIterations" value="1000"/>
21067 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21068 <param name="RANSACSamplingSize" value="10"/>
21069 <param name="estimateBestPeptides" value="false"/>
21070 <param name="InitialQualityCutoff" value="0.5"/>
21071 <param name="OverallQualityCutoff" value="5.5"/>
21072 <param name="NrRTBins" value="10"/>
21073 <param name="MinPeptidesPerBin" value="1"/>
21074 <param name="MinBinsFilled" value="8"/>
21075 <section name="lowess">
21076 <param name="span" value="0.05"/>
21077 </section>
21078 <section name="b_spline">
21079 <param name="num_nodes" value="5"/>
21080 </section>
21081 </section>
21082 <section name="Scoring">
21083 <param name="stop_report_after_feature" value="5"/>
21084 <param name="rt_normalization_factor" value="100.0"/>
21085 <param name="quantification_cutoff" value="0.0"/>
21086 <param name="write_convex_hull" value="false"/>
21087 <param name="spectrum_addition_method" value="simple"/>
21088 <param name="add_up_spectra" value="1"/>
21089 <param name="spacing_for_spectra_resampling" value="0.005"/>
21090 <param name="uis_threshold_sn" value="-1"/>
21091 <param name="uis_threshold_peak_area" value="0"/>
21092 <param name="scoring_model" value="default"/>
21093 <param name="im_extra_drift" value="0.0"/>
21094 <param name="strict" value="true"/>
21095 <section name="TransitionGroupPicker">
21096 <param name="stop_after_feature" value="-1"/>
21097 <param name="min_peak_width" value="-1.0"/>
21098 <param name="peak_integration" value="original"/>
21099 <param name="background_subtraction" value="none"/>
21100 <param name="recalculate_peaks" value="true"/>
21101 <param name="use_precursors" value="false"/>
21102 <param name="use_consensus" value="true"/>
21103 <param name="recalculate_peaks_max_z" value="0.75"/>
21104 <param name="minimal_quality" value="-1.5"/>
21105 <param name="resample_boundary" value="15.0"/>
21106 <param name="compute_peak_quality" value="false"/>
21107 <param name="compute_peak_shape_metrics" value="false"/>
21108 <param name="compute_total_mi" value="false"/>
21109 <param name="boundary_selection_method" value="largest"/>
21110 <section name="PeakPickerMRM">
21111 <param name="sgolay_frame_length" value="11"/>
21112 <param name="sgolay_polynomial_order" value="3"/>
21113 <param name="gauss_width" value="30.0"/>
21114 <param name="use_gauss" value="false"/>
21115 <param name="peak_width" value="-1.0"/>
21116 <param name="signal_to_noise" value="0.1"/>
21117 <param name="write_sn_log_messages" value="false"/>
21118 <param name="remove_overlapping_peaks" value="true"/>
21119 <param name="method" value="corrected"/>
21120 </section>
21121 <section name="PeakIntegrator">
21122 <param name="integration_type" value="intensity_sum"/>
21123 <param name="baseline_type" value="base_to_base"/>
21124 <param name="fit_EMG" value="false"/>
21125 </section>
21126 </section>
21127 <section name="DIAScoring">
21128 <param name="dia_extraction_window" value="0.05"/>
21129 <param name="dia_extraction_unit" value="Th"/>
21130 <param name="dia_centroided" value="false"/>
21131 <param name="dia_byseries_intensity_min" value="300.0"/>
21132 <param name="dia_byseries_ppm_diff" value="10.0"/>
21133 <param name="dia_nr_isotopes" value="4"/>
21134 <param name="dia_nr_charges" value="4"/>
21135 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21136 </section>
21137 <section name="EMGScoring">
21138 <param name="max_iteration" value="10"/>
21139 </section>
21140 <section name="Scores">
21141 <param name="use_shape_score" value="true"/>
21142 <param name="use_coelution_score" value="true"/>
21143 <param name="use_rt_score" value="true"/>
21144 <param name="use_library_score" value="true"/>
21145 <param name="use_intensity_score" value="true"/>
21146 <param name="use_nr_peaks_score" value="true"/>
21147 <param name="use_total_xic_score" value="true"/>
21148 <param name="use_total_mi_score" value="false"/>
21149 <param name="use_sn_score" value="true"/>
21150 <param name="use_mi_score" value="true"/>
21151 <param name="use_dia_scores" value="true"/>
21152 <param name="use_ms1_correlation" value="false"/>
21153 <param name="use_sonar_scores" value="true"/>
21154 <param name="use_ion_mobility_scores" value="false"/>
21155 <param name="use_ms1_fullscan" value="false"/>
21156 <param name="use_ms1_mi" value="true"/>
21157 <param name="use_uis_scores" value="false"/>
21158 </section>
21159 </section>
21160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21161 <output name="ctd_out" ftype="xml">
21162 <assert_contents>
21163 <is_valid_xml/>
21164 </assert_contents>
21165 </output>
21166 </test>
21167 <test expect_num_outputs="3">
21168 <conditional name="adv_opts_cond">
21169 <param name="adv_opts_selector" value="advanced"/>
21170 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21171 <param name="sort_swath_maps" value="false"/>
21172 <param name="enable_ms1" value="true"/>
21173 <param name="enable_ipf" value="true"/>
21174 <param name="out_chrom_type" value="mzML"/>
21175 <param name="min_upper_edge_dist" value="0.0"/>
21176 <param name="extra_rt_extraction_window" value="0.0"/>
21177 <param name="mz_extraction_window_unit" value="ppm"/>
21178 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21179 <param name="use_ms1_ion_mobility" value="true"/>
21180 <param name="matching_window_only" value="false"/>
21181 <param name="irt_mz_extraction_window" value="50.0"/>
21182 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21183 <param name="irt_im_extraction_window" value="-1.0"/>
21184 <param name="min_rsq" value="0.95"/>
21185 <param name="min_coverage" value="0.6"/>
21186 <param name="split_file_input" value="false"/>
21187 <param name="use_elution_model_score" value="false"/>
21188 <param name="readOptions" value="normal"/>
21189 <param name="mz_correction_function" value="none"/>
21190 <param name="extraction_function" value="tophat"/>
21191 <param name="batchSize" value="1000"/>
21192 <param name="ms1_isotopes" value="3"/>
21193 <param name="force" value="false"/>
21194 <param name="test" value="false"/>
21195 </conditional>
21196 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21197 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
21198 <param name="tr_type" value="pqp"/>
21199 <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
21200 <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21201 <param name="sonar" value="false"/>
21202 <param name="rt_extraction_window" value="600.0"/>
21203 <param name="ion_mobility_window" value="-1.0"/>
21204 <param name="mz_extraction_window" value="50.0"/>
21205 <param name="mz_extraction_window_ms1" value="50.0"/>
21206 <param name="im_extraction_window_ms1" value="-1.0"/>
21207 <section name="Debugging"/>
21208 <section name="Calibration">
21209 <param name="ms1_im_calibration" value="false"/>
21210 <param name="im_correction_function" value="linear"/>
21211 <param name="debug_im_file" value=""/>
21212 <param name="debug_mz_file" value=""/>
21213 </section>
21214 <section name="Library">
21215 <param name="retentionTimeInterpretation" value="iRT"/>
21216 <param name="override_group_label_check" value="false"/>
21217 <param name="force_invalid_mods" value="false"/>
21218 </section>
21219 <section name="RTNormalization">
21220 <param name="alignmentMethod" value="linear"/>
21221 <param name="outlierMethod" value="iter_residual"/>
21222 <param name="useIterativeChauvenet" value="false"/>
21223 <param name="RANSACMaxIterations" value="1000"/>
21224 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21225 <param name="RANSACSamplingSize" value="10"/>
21226 <param name="estimateBestPeptides" value="false"/>
21227 <param name="InitialQualityCutoff" value="0.5"/>
21228 <param name="OverallQualityCutoff" value="5.5"/>
21229 <param name="NrRTBins" value="10"/>
21230 <param name="MinPeptidesPerBin" value="1"/>
21231 <param name="MinBinsFilled" value="8"/>
21232 <section name="lowess">
21233 <param name="span" value="0.05"/>
21234 </section>
21235 <section name="b_spline">
21236 <param name="num_nodes" value="5"/>
21237 </section>
21238 </section>
21239 <section name="Scoring">
21240 <param name="stop_report_after_feature" value="5"/>
21241 <param name="rt_normalization_factor" value="100.0"/>
21242 <param name="quantification_cutoff" value="0.0"/>
21243 <param name="write_convex_hull" value="false"/>
21244 <param name="spectrum_addition_method" value="simple"/>
21245 <param name="add_up_spectra" value="1"/>
21246 <param name="spacing_for_spectra_resampling" value="0.005"/>
21247 <param name="uis_threshold_sn" value="-1"/>
21248 <param name="uis_threshold_peak_area" value="0"/>
21249 <param name="scoring_model" value="default"/>
21250 <param name="im_extra_drift" value="0.0"/>
21251 <param name="strict" value="true"/>
21252 <section name="TransitionGroupPicker">
21253 <param name="stop_after_feature" value="-1"/>
21254 <param name="min_peak_width" value="-1.0"/>
21255 <param name="peak_integration" value="original"/>
21256 <param name="background_subtraction" value="none"/>
21257 <param name="recalculate_peaks" value="true"/>
21258 <param name="use_precursors" value="false"/>
21259 <param name="use_consensus" value="true"/>
21260 <param name="recalculate_peaks_max_z" value="0.75"/>
21261 <param name="minimal_quality" value="-1.5"/>
21262 <param name="resample_boundary" value="15.0"/>
21263 <param name="compute_peak_quality" value="false"/>
21264 <param name="compute_peak_shape_metrics" value="false"/>
21265 <param name="compute_total_mi" value="false"/>
21266 <param name="boundary_selection_method" value="largest"/>
21267 <section name="PeakPickerMRM">
21268 <param name="sgolay_frame_length" value="11"/>
21269 <param name="sgolay_polynomial_order" value="3"/>
21270 <param name="gauss_width" value="30.0"/>
21271 <param name="use_gauss" value="false"/>
21272 <param name="peak_width" value="-1.0"/>
21273 <param name="signal_to_noise" value="0.1"/>
21274 <param name="write_sn_log_messages" value="false"/>
21275 <param name="remove_overlapping_peaks" value="true"/>
21276 <param name="method" value="corrected"/>
21277 </section>
21278 <section name="PeakIntegrator">
21279 <param name="integration_type" value="intensity_sum"/>
21280 <param name="baseline_type" value="base_to_base"/>
21281 <param name="fit_EMG" value="false"/>
21282 </section>
21283 </section>
21284 <section name="DIAScoring">
21285 <param name="dia_extraction_window" value="0.05"/>
21286 <param name="dia_extraction_unit" value="Th"/>
21287 <param name="dia_centroided" value="false"/>
21288 <param name="dia_byseries_intensity_min" value="300.0"/>
21289 <param name="dia_byseries_ppm_diff" value="10.0"/>
21290 <param name="dia_nr_isotopes" value="4"/>
21291 <param name="dia_nr_charges" value="4"/>
21292 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21293 </section>
21294 <section name="EMGScoring">
21295 <param name="max_iteration" value="10"/>
21296 </section>
21297 <section name="Scores">
21298 <param name="use_shape_score" value="true"/>
21299 <param name="use_coelution_score" value="true"/>
21300 <param name="use_rt_score" value="true"/>
21301 <param name="use_library_score" value="true"/>
21302 <param name="use_intensity_score" value="true"/>
21303 <param name="use_nr_peaks_score" value="true"/>
21304 <param name="use_total_xic_score" value="true"/>
21305 <param name="use_total_mi_score" value="false"/>
21306 <param name="use_sn_score" value="true"/>
21307 <param name="use_mi_score" value="true"/>
21308 <param name="use_dia_scores" value="true"/>
21309 <param name="use_ms1_correlation" value="false"/>
21310 <param name="use_sonar_scores" value="false"/>
21311 <param name="use_ion_mobility_scores" value="false"/>
21312 <param name="use_ms1_fullscan" value="false"/>
21313 <param name="use_ms1_mi" value="true"/>
21314 <param name="use_uis_scores" value="false"/>
21315 </section>
21316 </section>
21317 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
21318 <output name="ctd_out" ftype="xml">
21319 <assert_contents>
21320 <is_valid_xml/>
21321 </assert_contents>
21322 </output>
21323 </test>
21324 <test expect_num_outputs="3">
21325 <conditional name="adv_opts_cond">
21326 <param name="adv_opts_selector" value="advanced"/>
21327 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21328 <param name="sort_swath_maps" value="false"/>
21329 <param name="enable_ms1" value="true"/>
21330 <param name="enable_ipf" value="true"/>
21331 <param name="out_chrom_type" value="sqMass"/>
21332 <param name="min_upper_edge_dist" value="0.0"/>
21333 <param name="extra_rt_extraction_window" value="0.0"/>
21334 <param name="mz_extraction_window_unit" value="ppm"/>
21335 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21336 <param name="use_ms1_ion_mobility" value="true"/>
21337 <param name="matching_window_only" value="false"/>
21338 <param name="irt_mz_extraction_window" value="50.0"/>
21339 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21340 <param name="irt_im_extraction_window" value="-1.0"/>
21341 <param name="min_rsq" value="0.95"/>
21342 <param name="min_coverage" value="0.6"/>
21343 <param name="split_file_input" value="false"/>
21344 <param name="use_elution_model_score" value="false"/>
21345 <param name="readOptions" value="normal"/>
21346 <param name="mz_correction_function" value="none"/>
21347 <param name="extraction_function" value="tophat"/>
21348 <param name="batchSize" value="1000"/>
21349 <param name="ms1_isotopes" value="3"/>
21350 <param name="force" value="false"/>
21351 <param name="test" value="false"/>
21352 </conditional>
21353 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21354 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
21355 <param name="tr_type" value="pqp"/>
21356 <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
21357 <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
21358 <param name="sonar" value="false"/>
21359 <param name="rt_extraction_window" value="600.0"/>
21360 <param name="ion_mobility_window" value="-1.0"/>
21361 <param name="mz_extraction_window" value="50.0"/>
21362 <param name="mz_extraction_window_ms1" value="50.0"/>
21363 <param name="im_extraction_window_ms1" value="-1.0"/>
21364 <section name="Debugging"/>
21365 <section name="Calibration">
21366 <param name="ms1_im_calibration" value="false"/>
21367 <param name="im_correction_function" value="linear"/>
21368 <param name="debug_im_file" value=""/>
21369 <param name="debug_mz_file" value=""/>
21370 </section>
21371 <section name="Library">
21372 <param name="retentionTimeInterpretation" value="iRT"/>
21373 <param name="override_group_label_check" value="false"/>
21374 <param name="force_invalid_mods" value="false"/>
21375 </section>
21376 <section name="RTNormalization">
21377 <param name="alignmentMethod" value="linear"/>
21378 <param name="outlierMethod" value="iter_residual"/>
21379 <param name="useIterativeChauvenet" value="false"/>
21380 <param name="RANSACMaxIterations" value="1000"/>
21381 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21382 <param name="RANSACSamplingSize" value="10"/>
21383 <param name="estimateBestPeptides" value="false"/>
21384 <param name="InitialQualityCutoff" value="0.5"/>
21385 <param name="OverallQualityCutoff" value="5.5"/>
21386 <param name="NrRTBins" value="10"/>
21387 <param name="MinPeptidesPerBin" value="1"/>
21388 <param name="MinBinsFilled" value="8"/>
21389 <section name="lowess">
21390 <param name="span" value="0.05"/>
21391 </section>
21392 <section name="b_spline">
21393 <param name="num_nodes" value="5"/>
21394 </section>
21395 </section>
21396 <section name="Scoring">
21397 <param name="stop_report_after_feature" value="5"/>
21398 <param name="rt_normalization_factor" value="100.0"/>
21399 <param name="quantification_cutoff" value="0.0"/>
21400 <param name="write_convex_hull" value="false"/>
21401 <param name="spectrum_addition_method" value="simple"/>
21402 <param name="add_up_spectra" value="1"/>
21403 <param name="spacing_for_spectra_resampling" value="0.005"/>
21404 <param name="uis_threshold_sn" value="-1"/>
21405 <param name="uis_threshold_peak_area" value="0"/>
21406 <param name="scoring_model" value="default"/>
21407 <param name="im_extra_drift" value="0.0"/>
21408 <param name="strict" value="true"/>
21409 <section name="TransitionGroupPicker">
21410 <param name="stop_after_feature" value="-1"/>
21411 <param name="min_peak_width" value="-1.0"/>
21412 <param name="peak_integration" value="original"/>
21413 <param name="background_subtraction" value="none"/>
21414 <param name="recalculate_peaks" value="true"/>
21415 <param name="use_precursors" value="false"/>
21416 <param name="use_consensus" value="true"/>
21417 <param name="recalculate_peaks_max_z" value="0.75"/>
21418 <param name="minimal_quality" value="-1.5"/>
21419 <param name="resample_boundary" value="15.0"/>
21420 <param name="compute_peak_quality" value="false"/>
21421 <param name="compute_peak_shape_metrics" value="false"/>
21422 <param name="compute_total_mi" value="false"/>
21423 <param name="boundary_selection_method" value="largest"/>
21424 <section name="PeakPickerMRM">
21425 <param name="sgolay_frame_length" value="11"/>
21426 <param name="sgolay_polynomial_order" value="3"/>
21427 <param name="gauss_width" value="30.0"/>
21428 <param name="use_gauss" value="false"/>
21429 <param name="peak_width" value="-1.0"/>
21430 <param name="signal_to_noise" value="0.1"/>
21431 <param name="write_sn_log_messages" value="false"/>
21432 <param name="remove_overlapping_peaks" value="true"/>
21433 <param name="method" value="corrected"/>
21434 </section>
21435 <section name="PeakIntegrator">
21436 <param name="integration_type" value="intensity_sum"/>
21437 <param name="baseline_type" value="base_to_base"/>
21438 <param name="fit_EMG" value="false"/>
21439 </section>
21440 </section>
21441 <section name="DIAScoring">
21442 <param name="dia_extraction_window" value="0.05"/>
21443 <param name="dia_extraction_unit" value="Th"/>
21444 <param name="dia_centroided" value="false"/>
21445 <param name="dia_byseries_intensity_min" value="300.0"/>
21446 <param name="dia_byseries_ppm_diff" value="10.0"/>
21447 <param name="dia_nr_isotopes" value="4"/>
21448 <param name="dia_nr_charges" value="4"/>
21449 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21450 </section>
21451 <section name="EMGScoring">
21452 <param name="max_iteration" value="10"/>
21453 </section>
21454 <section name="Scores">
21455 <param name="use_shape_score" value="true"/>
21456 <param name="use_coelution_score" value="true"/>
21457 <param name="use_rt_score" value="true"/>
21458 <param name="use_library_score" value="true"/>
21459 <param name="use_intensity_score" value="true"/>
21460 <param name="use_nr_peaks_score" value="true"/>
21461 <param name="use_total_xic_score" value="true"/>
21462 <param name="use_total_mi_score" value="false"/>
21463 <param name="use_sn_score" value="true"/>
21464 <param name="use_mi_score" value="true"/>
21465 <param name="use_dia_scores" value="true"/>
21466 <param name="use_ms1_correlation" value="false"/>
21467 <param name="use_sonar_scores" value="false"/>
21468 <param name="use_ion_mobility_scores" value="false"/>
21469 <param name="use_ms1_fullscan" value="false"/>
21470 <param name="use_ms1_mi" value="true"/>
21471 <param name="use_uis_scores" value="false"/>
21472 </section>
21473 </section>
21474 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
21475 <output name="ctd_out" ftype="xml">
21476 <assert_contents>
21477 <is_valid_xml/>
21478 </assert_contents>
21479 </output>
21480 </test>
21481 <test expect_num_outputs="3">
21482 <conditional name="adv_opts_cond">
21483 <param name="adv_opts_selector" value="advanced"/>
21484 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21485 <param name="sort_swath_maps" value="false"/>
21486 <param name="enable_ms1" value="true"/>
21487 <param name="enable_ipf" value="true"/>
21488 <param name="out_chrom_type" value="mzML"/>
21489 <param name="min_upper_edge_dist" value="0.0"/>
21490 <param name="extra_rt_extraction_window" value="0.0"/>
21491 <param name="mz_extraction_window_unit" value="Th"/>
21492 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21493 <param name="use_ms1_ion_mobility" value="true"/>
21494 <param name="matching_window_only" value="false"/>
21495 <param name="irt_mz_extraction_window" value="50.0"/>
21496 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21497 <param name="irt_im_extraction_window" value="-1.0"/>
21498 <param name="min_rsq" value="0.95"/>
21499 <param name="min_coverage" value="0.6"/>
21500 <param name="split_file_input" value="false"/>
21501 <param name="use_elution_model_score" value="false"/>
21502 <param name="readOptions" value="normal"/>
21503 <param name="mz_correction_function" value="none"/>
21504 <param name="extraction_function" value="tophat"/>
21505 <param name="batchSize" value="1000"/>
21506 <param name="ms1_isotopes" value="2"/>
21507 <param name="force" value="false"/>
21508 <param name="test" value="true"/>
21509 </conditional>
21510 <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
21511 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21512 <param name="tr_type" value=""/>
21513 <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21514 <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21515 <param name="sonar" value="false"/>
21516 <param name="rt_extraction_window" value="600.0"/>
21517 <param name="ion_mobility_window" value="-1.0"/>
21518 <param name="mz_extraction_window" value="0.05"/>
21519 <param name="mz_extraction_window_ms1" value="50.0"/>
21520 <param name="im_extraction_window_ms1" value="-1.0"/>
21521 <section name="Debugging"/>
21522 <section name="Calibration">
21523 <param name="ms1_im_calibration" value="false"/>
21524 <param name="im_correction_function" value="linear"/>
21525 <param name="debug_im_file" value=""/>
21526 <param name="debug_mz_file" value=""/>
21527 </section>
21528 <section name="Library">
21529 <param name="retentionTimeInterpretation" value="iRT"/>
21530 <param name="override_group_label_check" value="false"/>
21531 <param name="force_invalid_mods" value="false"/>
21532 </section>
21533 <section name="RTNormalization">
21534 <param name="alignmentMethod" value="linear"/>
21535 <param name="outlierMethod" value="iter_residual"/>
21536 <param name="useIterativeChauvenet" value="false"/>
21537 <param name="RANSACMaxIterations" value="1000"/>
21538 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21539 <param name="RANSACSamplingSize" value="10"/>
21540 <param name="estimateBestPeptides" value="false"/>
21541 <param name="InitialQualityCutoff" value="0.5"/>
21542 <param name="OverallQualityCutoff" value="5.5"/>
21543 <param name="NrRTBins" value="10"/>
21544 <param name="MinPeptidesPerBin" value="1"/>
21545 <param name="MinBinsFilled" value="8"/>
21546 <section name="lowess">
21547 <param name="span" value="0.05"/>
21548 </section>
21549 <section name="b_spline">
21550 <param name="num_nodes" value="5"/>
21551 </section>
21552 </section>
21553 <section name="Scoring">
21554 <param name="stop_report_after_feature" value="5"/>
21555 <param name="rt_normalization_factor" value="100.0"/>
21556 <param name="quantification_cutoff" value="0.0"/>
21557 <param name="write_convex_hull" value="false"/>
21558 <param name="spectrum_addition_method" value="simple"/>
21559 <param name="add_up_spectra" value="1"/>
21560 <param name="spacing_for_spectra_resampling" value="0.005"/>
21561 <param name="uis_threshold_sn" value="-1"/>
21562 <param name="uis_threshold_peak_area" value="0"/>
21563 <param name="scoring_model" value="default"/>
21564 <param name="im_extra_drift" value="0.0"/>
21565 <param name="strict" value="true"/>
21566 <section name="TransitionGroupPicker">
21567 <param name="stop_after_feature" value="-1"/>
21568 <param name="min_peak_width" value="-1.0"/>
21569 <param name="peak_integration" value="original"/>
21570 <param name="background_subtraction" value="none"/>
21571 <param name="recalculate_peaks" value="true"/>
21572 <param name="use_precursors" value="true"/>
21573 <param name="use_consensus" value="true"/>
21574 <param name="recalculate_peaks_max_z" value="0.75"/>
21575 <param name="minimal_quality" value="-1.5"/>
21576 <param name="resample_boundary" value="15.0"/>
21577 <param name="compute_peak_quality" value="false"/>
21578 <param name="compute_peak_shape_metrics" value="false"/>
21579 <param name="compute_total_mi" value="false"/>
21580 <param name="boundary_selection_method" value="largest"/>
21581 <section name="PeakPickerMRM">
21582 <param name="sgolay_frame_length" value="11"/>
21583 <param name="sgolay_polynomial_order" value="3"/>
21584 <param name="gauss_width" value="30.0"/>
21585 <param name="use_gauss" value="false"/>
21586 <param name="peak_width" value="-1.0"/>
21587 <param name="signal_to_noise" value="0.1"/>
21588 <param name="write_sn_log_messages" value="false"/>
21589 <param name="remove_overlapping_peaks" value="true"/>
21590 <param name="method" value="corrected"/>
21591 </section>
21592 <section name="PeakIntegrator">
21593 <param name="integration_type" value="intensity_sum"/>
21594 <param name="baseline_type" value="base_to_base"/>
21595 <param name="fit_EMG" value="false"/>
21596 </section>
21597 </section>
21598 <section name="DIAScoring">
21599 <param name="dia_extraction_window" value="0.05"/>
21600 <param name="dia_extraction_unit" value="Th"/>
21601 <param name="dia_centroided" value="false"/>
21602 <param name="dia_byseries_intensity_min" value="300.0"/>
21603 <param name="dia_byseries_ppm_diff" value="10.0"/>
21604 <param name="dia_nr_isotopes" value="4"/>
21605 <param name="dia_nr_charges" value="4"/>
21606 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21607 </section>
21608 <section name="EMGScoring">
21609 <param name="max_iteration" value="10"/>
21610 </section>
21611 <section name="Scores">
21612 <param name="use_shape_score" value="true"/>
21613 <param name="use_coelution_score" value="true"/>
21614 <param name="use_rt_score" value="true"/>
21615 <param name="use_library_score" value="true"/>
21616 <param name="use_intensity_score" value="true"/>
21617 <param name="use_nr_peaks_score" value="true"/>
21618 <param name="use_total_xic_score" value="true"/>
21619 <param name="use_total_mi_score" value="false"/>
21620 <param name="use_sn_score" value="true"/>
21621 <param name="use_mi_score" value="false"/>
21622 <param name="use_dia_scores" value="true"/>
21623 <param name="use_ms1_correlation" value="false"/>
21624 <param name="use_sonar_scores" value="false"/>
21625 <param name="use_ion_mobility_scores" value="false"/>
21626 <param name="use_ms1_fullscan" value="false"/>
21627 <param name="use_ms1_mi" value="false"/>
21628 <param name="use_uis_scores" value="false"/>
21629 </section>
21630 </section>
21631 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21632 <output name="ctd_out" ftype="xml">
21633 <assert_contents>
21634 <is_valid_xml/>
21635 </assert_contents>
21636 </output>
21637 </test>
21638 <test expect_num_outputs="3">
21639 <conditional name="adv_opts_cond">
21640 <param name="adv_opts_selector" value="advanced"/>
21641 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21642 <param name="sort_swath_maps" value="false"/>
21643 <param name="enable_ms1" value="true"/>
21644 <param name="enable_ipf" value="true"/>
21645 <param name="out_chrom_type" value="mzML"/>
21646 <param name="min_upper_edge_dist" value="0.0"/>
21647 <param name="extra_rt_extraction_window" value="0.0"/>
21648 <param name="mz_extraction_window_unit" value="ppm"/>
21649 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21650 <param name="use_ms1_ion_mobility" value="true"/>
21651 <param name="matching_window_only" value="false"/>
21652 <param name="irt_mz_extraction_window" value="50.0"/>
21653 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21654 <param name="irt_im_extraction_window" value="-1.0"/>
21655 <param name="min_rsq" value="0.95"/>
21656 <param name="min_coverage" value="0.6"/>
21657 <param name="split_file_input" value="false"/>
21658 <param name="use_elution_model_score" value="false"/>
21659 <param name="readOptions" value="workingInMemory"/>
21660 <param name="mz_correction_function" value="none"/>
21661 <param name="extraction_function" value="tophat"/>
21662 <param name="batchSize" value="1000"/>
21663 <param name="ms1_isotopes" value="2"/>
21664 <param name="force" value="false"/>
21665 <param name="test" value="false"/>
21666 </conditional>
21667 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
21668 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21669 <param name="tr_type" value=""/>
21670 <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21671 <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21672 <param name="sonar" value="false"/>
21673 <param name="rt_extraction_window" value="600.0"/>
21674 <param name="ion_mobility_window" value="-1.0"/>
21675 <param name="mz_extraction_window" value="50.0"/>
21676 <param name="mz_extraction_window_ms1" value="50.0"/>
21677 <param name="im_extraction_window_ms1" value="-1.0"/>
21678 <section name="Debugging"/>
21679 <section name="Calibration">
21680 <param name="ms1_im_calibration" value="false"/>
21681 <param name="im_correction_function" value="linear"/>
21682 <param name="debug_im_file" value=""/>
21683 <param name="debug_mz_file" value=""/>
21684 </section>
21685 <section name="Library">
21686 <param name="retentionTimeInterpretation" value="iRT"/>
21687 <param name="override_group_label_check" value="false"/>
21688 <param name="force_invalid_mods" value="false"/>
21689 </section>
21690 <section name="RTNormalization">
21691 <param name="alignmentMethod" value="linear"/>
21692 <param name="outlierMethod" value="iter_residual"/>
21693 <param name="useIterativeChauvenet" value="false"/>
21694 <param name="RANSACMaxIterations" value="1000"/>
21695 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21696 <param name="RANSACSamplingSize" value="10"/>
21697 <param name="estimateBestPeptides" value="false"/>
21698 <param name="InitialQualityCutoff" value="0.5"/>
21699 <param name="OverallQualityCutoff" value="5.5"/>
21700 <param name="NrRTBins" value="10"/>
21701 <param name="MinPeptidesPerBin" value="1"/>
21702 <param name="MinBinsFilled" value="8"/>
21703 <section name="lowess">
21704 <param name="span" value="0.05"/>
21705 </section>
21706 <section name="b_spline">
21707 <param name="num_nodes" value="5"/>
21708 </section>
21709 </section>
21710 <section name="Scoring">
21711 <param name="stop_report_after_feature" value="5"/>
21712 <param name="rt_normalization_factor" value="100.0"/>
21713 <param name="quantification_cutoff" value="0.0"/>
21714 <param name="write_convex_hull" value="false"/>
21715 <param name="spectrum_addition_method" value="simple"/>
21716 <param name="add_up_spectra" value="1"/>
21717 <param name="spacing_for_spectra_resampling" value="0.005"/>
21718 <param name="uis_threshold_sn" value="-1"/>
21719 <param name="uis_threshold_peak_area" value="0"/>
21720 <param name="scoring_model" value="default"/>
21721 <param name="im_extra_drift" value="0.0"/>
21722 <param name="strict" value="true"/>
21723 <section name="TransitionGroupPicker">
21724 <param name="stop_after_feature" value="-1"/>
21725 <param name="min_peak_width" value="-1.0"/>
21726 <param name="peak_integration" value="original"/>
21727 <param name="background_subtraction" value="none"/>
21728 <param name="recalculate_peaks" value="true"/>
21729 <param name="use_precursors" value="false"/>
21730 <param name="use_consensus" value="true"/>
21731 <param name="recalculate_peaks_max_z" value="0.75"/>
21732 <param name="minimal_quality" value="-1.5"/>
21733 <param name="resample_boundary" value="15.0"/>
21734 <param name="compute_peak_quality" value="false"/>
21735 <param name="compute_peak_shape_metrics" value="false"/>
21736 <param name="compute_total_mi" value="false"/>
21737 <param name="boundary_selection_method" value="largest"/>
21738 <section name="PeakPickerMRM">
21739 <param name="sgolay_frame_length" value="11"/>
21740 <param name="sgolay_polynomial_order" value="3"/>
21741 <param name="gauss_width" value="30.0"/>
21742 <param name="use_gauss" value="false"/>
21743 <param name="peak_width" value="-1.0"/>
21744 <param name="signal_to_noise" value="0.1"/>
21745 <param name="write_sn_log_messages" value="false"/>
21746 <param name="remove_overlapping_peaks" value="true"/>
21747 <param name="method" value="corrected"/>
21748 </section>
21749 <section name="PeakIntegrator">
21750 <param name="integration_type" value="intensity_sum"/>
21751 <param name="baseline_type" value="base_to_base"/>
21752 <param name="fit_EMG" value="false"/>
21753 </section>
21754 </section>
21755 <section name="DIAScoring">
21756 <param name="dia_extraction_window" value="0.05"/>
21757 <param name="dia_extraction_unit" value="Th"/>
21758 <param name="dia_centroided" value="false"/>
21759 <param name="dia_byseries_intensity_min" value="300.0"/>
21760 <param name="dia_byseries_ppm_diff" value="10.0"/>
21761 <param name="dia_nr_isotopes" value="4"/>
21762 <param name="dia_nr_charges" value="4"/>
21763 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21764 </section>
21765 <section name="EMGScoring">
21766 <param name="max_iteration" value="10"/>
21767 </section>
21768 <section name="Scores">
21769 <param name="use_shape_score" value="true"/>
21770 <param name="use_coelution_score" value="true"/>
21771 <param name="use_rt_score" value="true"/>
21772 <param name="use_library_score" value="true"/>
21773 <param name="use_intensity_score" value="true"/>
21774 <param name="use_nr_peaks_score" value="true"/>
21775 <param name="use_total_xic_score" value="true"/>
21776 <param name="use_total_mi_score" value="false"/>
21777 <param name="use_sn_score" value="true"/>
21778 <param name="use_mi_score" value="true"/>
21779 <param name="use_dia_scores" value="true"/>
21780 <param name="use_ms1_correlation" value="false"/>
21781 <param name="use_sonar_scores" value="false"/>
21782 <param name="use_ion_mobility_scores" value="false"/>
21783 <param name="use_ms1_fullscan" value="false"/>
21784 <param name="use_ms1_mi" value="true"/>
21785 <param name="use_uis_scores" value="false"/>
21786 </section>
21787 </section>
21788 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21789 <output name="ctd_out" ftype="xml">
21790 <assert_contents>
21791 <is_valid_xml/>
21792 </assert_contents>
21793 </output>
21794 </test>
21795 <test expect_num_outputs="3">
21796 <conditional name="adv_opts_cond">
21797 <param name="adv_opts_selector" value="advanced"/>
21798 <param name="sort_swath_maps" value="false"/>
21799 <param name="enable_ms1" value="true"/>
21800 <param name="enable_ipf" value="true"/>
21801 <param name="out_chrom_type" value="mzML"/>
21802 <param name="min_upper_edge_dist" value="0.0"/>
21803 <param name="extra_rt_extraction_window" value="0.0"/>
21804 <param name="mz_extraction_window_unit" value="ppm"/>
21805 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21806 <param name="use_ms1_ion_mobility" value="false"/>
21807 <param name="matching_window_only" value="false"/>
21808 <param name="irt_mz_extraction_window" value="50.0"/>
21809 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21810 <param name="irt_im_extraction_window" value="-1.0"/>
21811 <param name="min_rsq" value="0.95"/>
21812 <param name="min_coverage" value="0.6"/>
21813 <param name="split_file_input" value="false"/>
21814 <param name="use_elution_model_score" value="false"/>
21815 <param name="readOptions" value="workingInMemory"/>
21816 <param name="mz_correction_function" value="none"/>
21817 <param name="extraction_function" value="tophat"/>
21818 <param name="batchSize" value="1000"/>
21819 <param name="ms1_isotopes" value="3"/>
21820 <param name="force" value="false"/>
21821 <param name="test" value="false"/>
21822 </conditional>
21823 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21824 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21825 <param name="tr_type" value=""/>
21826 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21827 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21828 <param name="sonar" value="false"/>
21829 <param name="rt_extraction_window" value="600.0"/>
21830 <param name="ion_mobility_window" value="0.05"/>
21831 <param name="mz_extraction_window" value="50.0"/>
21832 <param name="mz_extraction_window_ms1" value="50.0"/>
21833 <param name="im_extraction_window_ms1" value="-1.0"/>
21834 <section name="Debugging"/>
21835 <section name="Calibration">
21836 <param name="ms1_im_calibration" value="false"/>
21837 <param name="im_correction_function" value="linear"/>
21838 <param name="debug_im_file" value=""/>
21839 <param name="debug_mz_file" value=""/>
21840 </section>
21841 <section name="Library">
21842 <param name="retentionTimeInterpretation" value="iRT"/>
21843 <param name="override_group_label_check" value="false"/>
21844 <param name="force_invalid_mods" value="false"/>
21845 </section>
21846 <section name="RTNormalization">
21847 <param name="alignmentMethod" value="linear"/>
21848 <param name="outlierMethod" value="iter_residual"/>
21849 <param name="useIterativeChauvenet" value="false"/>
21850 <param name="RANSACMaxIterations" value="1000"/>
21851 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21852 <param name="RANSACSamplingSize" value="10"/>
21853 <param name="estimateBestPeptides" value="false"/>
21854 <param name="InitialQualityCutoff" value="0.5"/>
21855 <param name="OverallQualityCutoff" value="5.5"/>
21856 <param name="NrRTBins" value="10"/>
21857 <param name="MinPeptidesPerBin" value="1"/>
21858 <param name="MinBinsFilled" value="8"/>
21859 <section name="lowess">
21860 <param name="span" value="0.05"/>
21861 </section>
21862 <section name="b_spline">
21863 <param name="num_nodes" value="5"/>
21864 </section>
21865 </section>
21866 <section name="Scoring">
21867 <param name="stop_report_after_feature" value="5"/>
21868 <param name="rt_normalization_factor" value="100.0"/>
21869 <param name="quantification_cutoff" value="0.0"/>
21870 <param name="write_convex_hull" value="false"/>
21871 <param name="spectrum_addition_method" value="simple"/>
21872 <param name="add_up_spectra" value="1"/>
21873 <param name="spacing_for_spectra_resampling" value="0.005"/>
21874 <param name="uis_threshold_sn" value="-1"/>
21875 <param name="uis_threshold_peak_area" value="0"/>
21876 <param name="scoring_model" value="default"/>
21877 <param name="im_extra_drift" value="0.0"/>
21878 <param name="strict" value="true"/>
21879 <section name="TransitionGroupPicker">
21880 <param name="stop_after_feature" value="-1"/>
21881 <param name="min_peak_width" value="-1.0"/>
21882 <param name="peak_integration" value="original"/>
21883 <param name="background_subtraction" value="none"/>
21884 <param name="recalculate_peaks" value="true"/>
21885 <param name="use_precursors" value="false"/>
21886 <param name="use_consensus" value="true"/>
21887 <param name="recalculate_peaks_max_z" value="0.75"/>
21888 <param name="minimal_quality" value="-1.5"/>
21889 <param name="resample_boundary" value="15.0"/>
21890 <param name="compute_peak_quality" value="false"/>
21891 <param name="compute_peak_shape_metrics" value="false"/>
21892 <param name="compute_total_mi" value="false"/>
21893 <param name="boundary_selection_method" value="largest"/>
21894 <section name="PeakPickerMRM">
21895 <param name="sgolay_frame_length" value="11"/>
21896 <param name="sgolay_polynomial_order" value="3"/>
21897 <param name="gauss_width" value="30.0"/>
21898 <param name="use_gauss" value="false"/>
21899 <param name="peak_width" value="-1.0"/>
21900 <param name="signal_to_noise" value="0.1"/>
21901 <param name="write_sn_log_messages" value="false"/>
21902 <param name="remove_overlapping_peaks" value="true"/>
21903 <param name="method" value="corrected"/>
21904 </section>
21905 <section name="PeakIntegrator">
21906 <param name="integration_type" value="intensity_sum"/>
21907 <param name="baseline_type" value="base_to_base"/>
21908 <param name="fit_EMG" value="false"/>
21909 </section>
21910 </section>
21911 <section name="DIAScoring">
21912 <param name="dia_extraction_window" value="0.05"/>
21913 <param name="dia_extraction_unit" value="Th"/>
21914 <param name="dia_centroided" value="false"/>
21915 <param name="dia_byseries_intensity_min" value="300.0"/>
21916 <param name="dia_byseries_ppm_diff" value="10.0"/>
21917 <param name="dia_nr_isotopes" value="4"/>
21918 <param name="dia_nr_charges" value="4"/>
21919 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21920 </section>
21921 <section name="EMGScoring">
21922 <param name="max_iteration" value="10"/>
21923 </section>
21924 <section name="Scores">
21925 <param name="use_shape_score" value="true"/>
21926 <param name="use_coelution_score" value="true"/>
21927 <param name="use_rt_score" value="true"/>
21928 <param name="use_library_score" value="true"/>
21929 <param name="use_intensity_score" value="true"/>
21930 <param name="use_nr_peaks_score" value="true"/>
21931 <param name="use_total_xic_score" value="true"/>
21932 <param name="use_total_mi_score" value="false"/>
21933 <param name="use_sn_score" value="true"/>
21934 <param name="use_mi_score" value="true"/>
21935 <param name="use_dia_scores" value="true"/>
21936 <param name="use_ms1_correlation" value="false"/>
21937 <param name="use_sonar_scores" value="false"/>
21938 <param name="use_ion_mobility_scores" value="true"/>
21939 <param name="use_ms1_fullscan" value="false"/>
21940 <param name="use_ms1_mi" value="true"/>
21941 <param name="use_uis_scores" value="false"/>
21942 </section>
21943 </section>
21944 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21945 <output name="ctd_out" ftype="xml">
21946 <assert_contents>
21947 <is_valid_xml/>
21948 </assert_contents>
21949 </output>
21950 </test>
21951 <test expect_num_outputs="3">
21952 <conditional name="adv_opts_cond">
21953 <param name="adv_opts_selector" value="advanced"/>
21954 <param name="sort_swath_maps" value="false"/>
21955 <param name="enable_ms1" value="true"/>
21956 <param name="enable_ipf" value="true"/>
21957 <param name="out_chrom_type" value="mzML"/>
21958 <param name="min_upper_edge_dist" value="0.0"/>
21959 <param name="extra_rt_extraction_window" value="0.0"/>
21960 <param name="mz_extraction_window_unit" value="ppm"/>
21961 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
21962 <param name="use_ms1_ion_mobility" value="false"/>
21963 <param name="matching_window_only" value="false"/>
21964 <param name="irt_mz_extraction_window" value="50.0"/>
21965 <param name="irt_mz_extraction_window_unit" value="ppm"/>
21966 <param name="irt_im_extraction_window" value="-1.0"/>
21967 <param name="min_rsq" value="0.95"/>
21968 <param name="min_coverage" value="0.6"/>
21969 <param name="split_file_input" value="false"/>
21970 <param name="use_elution_model_score" value="false"/>
21971 <param name="readOptions" value="cache"/>
21972 <param name="mz_correction_function" value="none"/>
21973 <param name="extraction_function" value="tophat"/>
21974 <param name="batchSize" value="1000"/>
21975 <param name="ms1_isotopes" value="3"/>
21976 <param name="force" value="false"/>
21977 <param name="test" value="false"/>
21978 </conditional>
21979 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21980 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21981 <param name="tr_type" value=""/>
21982 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21983 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21984 <param name="sonar" value="false"/>
21985 <param name="rt_extraction_window" value="600.0"/>
21986 <param name="ion_mobility_window" value="0.05"/>
21987 <param name="mz_extraction_window" value="50.0"/>
21988 <param name="mz_extraction_window_ms1" value="50.0"/>
21989 <param name="im_extraction_window_ms1" value="-1.0"/>
21990 <section name="Debugging"/>
21991 <section name="Calibration">
21992 <param name="ms1_im_calibration" value="false"/>
21993 <param name="im_correction_function" value="linear"/>
21994 <param name="debug_im_file" value=""/>
21995 <param name="debug_mz_file" value=""/>
21996 </section>
21997 <section name="Library">
21998 <param name="retentionTimeInterpretation" value="iRT"/>
21999 <param name="override_group_label_check" value="false"/>
22000 <param name="force_invalid_mods" value="false"/>
22001 </section>
22002 <section name="RTNormalization">
22003 <param name="alignmentMethod" value="linear"/>
22004 <param name="outlierMethod" value="iter_residual"/>
22005 <param name="useIterativeChauvenet" value="false"/>
22006 <param name="RANSACMaxIterations" value="1000"/>
22007 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22008 <param name="RANSACSamplingSize" value="10"/>
22009 <param name="estimateBestPeptides" value="false"/>
22010 <param name="InitialQualityCutoff" value="0.5"/>
22011 <param name="OverallQualityCutoff" value="5.5"/>
22012 <param name="NrRTBins" value="10"/>
22013 <param name="MinPeptidesPerBin" value="1"/>
22014 <param name="MinBinsFilled" value="8"/>
22015 <section name="lowess">
22016 <param name="span" value="0.05"/>
22017 </section>
22018 <section name="b_spline">
22019 <param name="num_nodes" value="5"/>
22020 </section>
22021 </section>
22022 <section name="Scoring">
22023 <param name="stop_report_after_feature" value="5"/>
22024 <param name="rt_normalization_factor" value="100.0"/>
22025 <param name="quantification_cutoff" value="0.0"/>
22026 <param name="write_convex_hull" value="false"/>
22027 <param name="spectrum_addition_method" value="simple"/>
22028 <param name="add_up_spectra" value="1"/>
22029 <param name="spacing_for_spectra_resampling" value="0.005"/>
22030 <param name="uis_threshold_sn" value="-1"/>
22031 <param name="uis_threshold_peak_area" value="0"/>
22032 <param name="scoring_model" value="default"/>
22033 <param name="im_extra_drift" value="0.0"/>
22034 <param name="strict" value="true"/>
22035 <section name="TransitionGroupPicker">
22036 <param name="stop_after_feature" value="-1"/>
22037 <param name="min_peak_width" value="-1.0"/>
22038 <param name="peak_integration" value="original"/>
22039 <param name="background_subtraction" value="none"/>
22040 <param name="recalculate_peaks" value="true"/>
22041 <param name="use_precursors" value="false"/>
22042 <param name="use_consensus" value="true"/>
22043 <param name="recalculate_peaks_max_z" value="0.75"/>
22044 <param name="minimal_quality" value="-1.5"/>
22045 <param name="resample_boundary" value="15.0"/>
22046 <param name="compute_peak_quality" value="false"/>
22047 <param name="compute_peak_shape_metrics" value="false"/>
22048 <param name="compute_total_mi" value="false"/>
22049 <param name="boundary_selection_method" value="largest"/>
22050 <section name="PeakPickerMRM">
22051 <param name="sgolay_frame_length" value="11"/>
22052 <param name="sgolay_polynomial_order" value="3"/>
22053 <param name="gauss_width" value="30.0"/>
22054 <param name="use_gauss" value="false"/>
22055 <param name="peak_width" value="-1.0"/>
22056 <param name="signal_to_noise" value="0.1"/>
22057 <param name="write_sn_log_messages" value="false"/>
22058 <param name="remove_overlapping_peaks" value="true"/>
22059 <param name="method" value="corrected"/>
22060 </section>
22061 <section name="PeakIntegrator">
22062 <param name="integration_type" value="intensity_sum"/>
22063 <param name="baseline_type" value="base_to_base"/>
22064 <param name="fit_EMG" value="false"/>
22065 </section>
22066 </section>
22067 <section name="DIAScoring">
22068 <param name="dia_extraction_window" value="0.05"/>
22069 <param name="dia_extraction_unit" value="Th"/>
22070 <param name="dia_centroided" value="false"/>
22071 <param name="dia_byseries_intensity_min" value="300.0"/>
22072 <param name="dia_byseries_ppm_diff" value="10.0"/>
22073 <param name="dia_nr_isotopes" value="4"/>
22074 <param name="dia_nr_charges" value="4"/>
22075 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22076 </section>
22077 <section name="EMGScoring">
22078 <param name="max_iteration" value="10"/>
22079 </section>
22080 <section name="Scores">
22081 <param name="use_shape_score" value="true"/>
22082 <param name="use_coelution_score" value="true"/>
22083 <param name="use_rt_score" value="true"/>
22084 <param name="use_library_score" value="true"/>
22085 <param name="use_intensity_score" value="true"/>
22086 <param name="use_nr_peaks_score" value="true"/>
22087 <param name="use_total_xic_score" value="true"/>
22088 <param name="use_total_mi_score" value="false"/>
22089 <param name="use_sn_score" value="true"/>
22090 <param name="use_mi_score" value="true"/>
22091 <param name="use_dia_scores" value="true"/>
22092 <param name="use_ms1_correlation" value="false"/>
22093 <param name="use_sonar_scores" value="false"/>
22094 <param name="use_ion_mobility_scores" value="true"/>
22095 <param name="use_ms1_fullscan" value="false"/>
22096 <param name="use_ms1_mi" value="true"/>
22097 <param name="use_uis_scores" value="false"/>
22098 </section>
22099 </section>
22100 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22101 <output name="ctd_out" ftype="xml">
22102 <assert_contents>
22103 <is_valid_xml/>
22104 </assert_contents>
22105 </output>
22106 </test>
22107 <test expect_num_outputs="3">
22108 <conditional name="adv_opts_cond">
22109 <param name="adv_opts_selector" value="advanced"/>
22110 <param name="sort_swath_maps" value="false"/>
22111 <param name="enable_ms1" value="true"/>
22112 <param name="enable_ipf" value="true"/>
22113 <param name="out_chrom_type" value="mzML"/>
22114 <param name="min_upper_edge_dist" value="0.0"/>
22115 <param name="extra_rt_extraction_window" value="0.0"/>
22116 <param name="mz_extraction_window_unit" value="ppm"/>
22117 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22118 <param name="use_ms1_ion_mobility" value="false"/>
22119 <param name="matching_window_only" value="false"/>
22120 <param name="irt_mz_extraction_window" value="50.0"/>
22121 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22122 <param name="irt_im_extraction_window" value="-1.0"/>
22123 <param name="min_rsq" value="0.95"/>
22124 <param name="min_coverage" value="0.6"/>
22125 <param name="split_file_input" value="false"/>
22126 <param name="use_elution_model_score" value="false"/>
22127 <param name="readOptions" value="workingInMemory"/>
22128 <param name="mz_correction_function" value="none"/>
22129 <param name="extraction_function" value="tophat"/>
22130 <param name="batchSize" value="1000"/>
22131 <param name="ms1_isotopes" value="3"/>
22132 <param name="force" value="false"/>
22133 <param name="test" value="false"/>
22134 </conditional>
22135 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
22136 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
22137 <param name="tr_type" value="pqp"/>
22138 <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22139 <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22140 <param name="sonar" value="false"/>
22141 <param name="rt_extraction_window" value="600.0"/>
22142 <param name="ion_mobility_window" value="0.05"/>
22143 <param name="mz_extraction_window" value="50.0"/>
22144 <param name="mz_extraction_window_ms1" value="50.0"/>
22145 <param name="im_extraction_window_ms1" value="-1.0"/>
22146 <section name="Debugging"/>
22147 <section name="Calibration">
22148 <param name="ms1_im_calibration" value="false"/>
22149 <param name="im_correction_function" value="linear"/>
22150 <param name="debug_im_file" value=""/>
22151 <param name="debug_mz_file" value=""/>
22152 </section>
22153 <section name="Library">
22154 <param name="retentionTimeInterpretation" value="iRT"/>
22155 <param name="override_group_label_check" value="false"/>
22156 <param name="force_invalid_mods" value="false"/>
22157 </section>
22158 <section name="RTNormalization">
22159 <param name="alignmentMethod" value="linear"/>
22160 <param name="outlierMethod" value="iter_residual"/>
22161 <param name="useIterativeChauvenet" value="false"/>
22162 <param name="RANSACMaxIterations" value="1000"/>
22163 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22164 <param name="RANSACSamplingSize" value="10"/>
22165 <param name="estimateBestPeptides" value="false"/>
22166 <param name="InitialQualityCutoff" value="0.5"/>
22167 <param name="OverallQualityCutoff" value="5.5"/>
22168 <param name="NrRTBins" value="10"/>
22169 <param name="MinPeptidesPerBin" value="1"/>
22170 <param name="MinBinsFilled" value="8"/>
22171 <section name="lowess">
22172 <param name="span" value="0.05"/>
22173 </section>
22174 <section name="b_spline">
22175 <param name="num_nodes" value="5"/>
22176 </section>
22177 </section>
22178 <section name="Scoring">
22179 <param name="stop_report_after_feature" value="5"/>
22180 <param name="rt_normalization_factor" value="100.0"/>
22181 <param name="quantification_cutoff" value="0.0"/>
22182 <param name="write_convex_hull" value="false"/>
22183 <param name="spectrum_addition_method" value="simple"/>
22184 <param name="add_up_spectra" value="1"/>
22185 <param name="spacing_for_spectra_resampling" value="0.005"/>
22186 <param name="uis_threshold_sn" value="-1"/>
22187 <param name="uis_threshold_peak_area" value="0"/>
22188 <param name="scoring_model" value="default"/>
22189 <param name="im_extra_drift" value="0.0"/>
22190 <param name="strict" value="true"/>
22191 <section name="TransitionGroupPicker">
22192 <param name="stop_after_feature" value="-1"/>
22193 <param name="min_peak_width" value="-1.0"/>
22194 <param name="peak_integration" value="original"/>
22195 <param name="background_subtraction" value="none"/>
22196 <param name="recalculate_peaks" value="true"/>
22197 <param name="use_precursors" value="false"/>
22198 <param name="use_consensus" value="true"/>
22199 <param name="recalculate_peaks_max_z" value="0.75"/>
22200 <param name="minimal_quality" value="-1.5"/>
22201 <param name="resample_boundary" value="15.0"/>
22202 <param name="compute_peak_quality" value="false"/>
22203 <param name="compute_peak_shape_metrics" value="false"/>
22204 <param name="compute_total_mi" value="false"/>
22205 <param name="boundary_selection_method" value="largest"/>
22206 <section name="PeakPickerMRM">
22207 <param name="sgolay_frame_length" value="11"/>
22208 <param name="sgolay_polynomial_order" value="3"/>
22209 <param name="gauss_width" value="30.0"/>
22210 <param name="use_gauss" value="false"/>
22211 <param name="peak_width" value="-1.0"/>
22212 <param name="signal_to_noise" value="0.1"/>
22213 <param name="write_sn_log_messages" value="false"/>
22214 <param name="remove_overlapping_peaks" value="true"/>
22215 <param name="method" value="corrected"/>
22216 </section>
22217 <section name="PeakIntegrator">
22218 <param name="integration_type" value="intensity_sum"/>
22219 <param name="baseline_type" value="base_to_base"/>
22220 <param name="fit_EMG" value="false"/>
22221 </section>
22222 </section>
22223 <section name="DIAScoring">
22224 <param name="dia_extraction_window" value="0.05"/>
22225 <param name="dia_extraction_unit" value="Th"/>
22226 <param name="dia_centroided" value="false"/>
22227 <param name="dia_byseries_intensity_min" value="300.0"/>
22228 <param name="dia_byseries_ppm_diff" value="10.0"/>
22229 <param name="dia_nr_isotopes" value="4"/>
22230 <param name="dia_nr_charges" value="4"/>
22231 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22232 </section>
22233 <section name="EMGScoring">
22234 <param name="max_iteration" value="10"/>
22235 </section>
22236 <section name="Scores">
22237 <param name="use_shape_score" value="true"/>
22238 <param name="use_coelution_score" value="true"/>
22239 <param name="use_rt_score" value="true"/>
22240 <param name="use_library_score" value="true"/>
22241 <param name="use_intensity_score" value="true"/>
22242 <param name="use_nr_peaks_score" value="true"/>
22243 <param name="use_total_xic_score" value="true"/>
22244 <param name="use_total_mi_score" value="false"/>
22245 <param name="use_sn_score" value="true"/>
22246 <param name="use_mi_score" value="true"/>
22247 <param name="use_dia_scores" value="true"/>
22248 <param name="use_ms1_correlation" value="false"/>
22249 <param name="use_sonar_scores" value="false"/>
22250 <param name="use_ion_mobility_scores" value="false"/>
22251 <param name="use_ms1_fullscan" value="false"/>
22252 <param name="use_ms1_mi" value="true"/>
22253 <param name="use_uis_scores" value="false"/>
22254 </section>
22255 </section>
22256 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22257 <output name="ctd_out" ftype="xml">
22258 <assert_contents>
22259 <is_valid_xml/>
22260 </assert_contents>
22261 </output>
22262 </test>
22263 <test expect_num_outputs="2">
22264 <conditional name="adv_opts_cond">
22265 <param name="adv_opts_selector" value="advanced"/>
22266 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
22267 <param name="sort_swath_maps" value="false"/>
22268 <param name="enable_ms1" value="true"/>
22269 <param name="enable_ipf" value="true"/>
22270 <param name="min_upper_edge_dist" value="0.0"/>
22271 <param name="extra_rt_extraction_window" value="0.0"/>
22272 <param name="mz_extraction_window_unit" value="Th"/>
22273 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
22274 <param name="use_ms1_ion_mobility" value="true"/>
22275 <param name="matching_window_only" value="false"/>
22276 <param name="irt_mz_extraction_window" value="50.0"/>
22277 <param name="irt_mz_extraction_window_unit" value="ppm"/>
22278 <param name="irt_im_extraction_window" value="-1.0"/>
22279 <param name="min_rsq" value="0.95"/>
22280 <param name="min_coverage" value="0.6"/>
22281 <param name="split_file_input" value="false"/>
22282 <param name="use_elution_model_score" value="false"/>
22283 <param name="readOptions" value="normal"/>
22284 <param name="mz_correction_function" value="none"/>
22285 <param name="extraction_function" value="tophat"/>
22286 <param name="batchSize" value="1000"/>
22287 <param name="ms1_isotopes" value="0"/>
22288 <param name="force" value="false"/>
22289 <param name="test" value="true"/>
22290 </conditional>
22291 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
22292 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
22293 <param name="tr_type" value=""/>
22294 <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22295 <param name="sonar" value="false"/>
22296 <param name="rt_extraction_window" value="600.0"/>
22297 <param name="ion_mobility_window" value="-1.0"/>
22298 <param name="mz_extraction_window" value="0.05"/>
22299 <param name="mz_extraction_window_ms1" value="50.0"/>
22300 <param name="im_extraction_window_ms1" value="-1.0"/>
22301 <section name="Debugging"/>
22302 <section name="Calibration">
22303 <param name="ms1_im_calibration" value="false"/>
22304 <param name="im_correction_function" value="linear"/>
22305 <param name="debug_im_file" value=""/>
22306 <param name="debug_mz_file" value=""/>
22307 </section>
22308 <section name="Library">
22309 <param name="retentionTimeInterpretation" value="iRT"/>
22310 <param name="override_group_label_check" value="false"/>
22311 <param name="force_invalid_mods" value="false"/>
22312 </section>
22313 <section name="RTNormalization">
22314 <param name="alignmentMethod" value="linear"/>
22315 <param name="outlierMethod" value="iter_residual"/>
22316 <param name="useIterativeChauvenet" value="false"/>
22317 <param name="RANSACMaxIterations" value="1000"/>
22318 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22319 <param name="RANSACSamplingSize" value="10"/>
22320 <param name="estimateBestPeptides" value="false"/>
22321 <param name="InitialQualityCutoff" value="0.5"/>
22322 <param name="OverallQualityCutoff" value="5.5"/>
22323 <param name="NrRTBins" value="10"/>
22324 <param name="MinPeptidesPerBin" value="1"/>
22325 <param name="MinBinsFilled" value="8"/>
22326 <section name="lowess">
22327 <param name="span" value="0.05"/>
22328 </section>
22329 <section name="b_spline">
22330 <param name="num_nodes" value="5"/>
22331 </section>
22332 </section>
22333 <section name="Scoring">
22334 <param name="stop_report_after_feature" value="5"/>
22335 <param name="rt_normalization_factor" value="100.0"/>
22336 <param name="quantification_cutoff" value="0.0"/>
22337 <param name="write_convex_hull" value="false"/>
22338 <param name="spectrum_addition_method" value="simple"/>
22339 <param name="add_up_spectra" value="1"/>
22340 <param name="spacing_for_spectra_resampling" value="0.005"/>
22341 <param name="uis_threshold_sn" value="-1"/>
22342 <param name="uis_threshold_peak_area" value="0"/>
22343 <param name="scoring_model" value="default"/>
22344 <param name="im_extra_drift" value="0.0"/>
22345 <param name="strict" value="true"/>
19015 <section name="TransitionGroupPicker"> 22346 <section name="TransitionGroupPicker">
19016 <param name="stop_after_feature" value="-1"/> 22347 <param name="stop_after_feature" value="-1"/>
19017 <param name="min_peak_width" value="-1.0"/> 22348 <param name="min_peak_width" value="-1.0"/>
19018 <param name="peak_integration" value="original"/> 22349 <param name="peak_integration" value="original"/>
19019 <param name="background_subtraction" value="none"/> 22350 <param name="background_subtraction" value="none"/>
19071 <param name="use_dia_scores" value="true"/> 22402 <param name="use_dia_scores" value="true"/>
19072 <param name="use_ms1_correlation" value="false"/> 22403 <param name="use_ms1_correlation" value="false"/>
19073 <param name="use_sonar_scores" value="false"/> 22404 <param name="use_sonar_scores" value="false"/>
19074 <param name="use_ion_mobility_scores" value="false"/> 22405 <param name="use_ion_mobility_scores" value="false"/>
19075 <param name="use_ms1_fullscan" value="false"/> 22406 <param name="use_ms1_fullscan" value="false"/>
19076 <param name="use_ms1_mi" value="false"/> 22407 <param name="use_ms1_mi" value="true"/>
19077 <param name="use_uis_scores" value="false"/> 22408 <param name="use_uis_scores" value="false"/>
19078 </section> 22409 </section>
19079 </section> 22410 </section>
19080 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> 22411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
19081 <output name="ctd_out" ftype="xml"> 22412 <output name="ctd_out" ftype="xml">
19082 <assert_contents> 22413 <assert_contents>
19083 <is_valid_xml/> 22414 <is_valid_xml/>
19084 </assert_contents> 22415 </assert_contents>
19085 </output> 22416 </output>
19086 </test> 22417 </test>
19087 <test expect_num_outputs="3"> 22418 <test expect_num_outputs="2">
19088 <conditional name="adv_opts_cond"> 22419 <conditional name="adv_opts_cond">
19089 <param name="adv_opts_selector" value="advanced"/> 22420 <param name="adv_opts_selector" value="advanced"/>
19090 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> 22421 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19091 <param name="sort_swath_maps" value="false"/> 22422 <param name="sort_swath_maps" value="false"/>
19092 <param name="use_ms1_traces" value="false"/> 22423 <param name="enable_ms1" value="true"/>
19093 <param name="enable_uis_scoring" value="false"/> 22424 <param name="enable_ipf" value="true"/>
19094 <param name="out_chrom_type" value="mzML"/>
19095 <param name="min_upper_edge_dist" value="0.0"/> 22425 <param name="min_upper_edge_dist" value="0.0"/>
19096 <param name="extra_rt_extraction_window" value="0.0"/> 22426 <param name="extra_rt_extraction_window" value="0.0"/>
19097 <param name="mz_extraction_window_unit" value="Th"/> 22427 <param name="mz_extraction_window_unit" value="Th"/>
19098 <param name="mz_extraction_window_ms1_unit" value="Th"/> 22428 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19099 <param name="use_ms1_ion_mobility" value="true"/> 22429 <param name="use_ms1_ion_mobility" value="true"/>
19100 <param name="matching_window_only" value="false"/> 22430 <param name="matching_window_only" value="false"/>
19101 <param name="irt_mz_extraction_window" value="0.05"/> 22431 <param name="irt_mz_extraction_window" value="50.0"/>
19102 <param name="irt_mz_extraction_window_unit" value="Th"/> 22432 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19103 <param name="irt_im_extraction_window" value="-1.0"/> 22433 <param name="irt_im_extraction_window" value="-1.0"/>
19104 <param name="min_rsq" value="0.95"/> 22434 <param name="min_rsq" value="0.95"/>
19105 <param name="min_coverage" value="0.6"/> 22435 <param name="min_coverage" value="0.6"/>
19106 <param name="split_file_input" value="false"/> 22436 <param name="split_file_input" value="false"/>
19107 <param name="use_elution_model_score" value="false"/> 22437 <param name="use_elution_model_score" value="false"/>
19108 <param name="readOptions" value="normal"/> 22438 <param name="readOptions" value="normal"/>
19109 <param name="mz_correction_function" value="none"/> 22439 <param name="mz_correction_function" value="none"/>
19110 <param name="extraction_function" value="tophat"/> 22440 <param name="extraction_function" value="tophat"/>
19111 <param name="batchSize" value="250"/> 22441 <param name="batchSize" value="1000"/>
19112 <param name="ms1_isotopes" value="0"/> 22442 <param name="ms1_isotopes" value="0"/>
19113 <param name="force" value="false"/> 22443 <param name="force" value="false"/>
19114 <param name="test" value="true"/> 22444 <param name="test" value="true"/>
19115 </conditional> 22445 </conditional>
19116 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> 22446 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19117 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> 22447 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19118 <param name="tr_type" value=""/> 22448 <param name="tr_type" value=""/>
19119 <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> 22449 <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19120 <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19121 <param name="sonar" value="false"/> 22450 <param name="sonar" value="false"/>
19122 <param name="rt_extraction_window" value="600.0"/> 22451 <param name="rt_extraction_window" value="600.0"/>
19123 <param name="ion_mobility_window" value="-1.0"/> 22452 <param name="ion_mobility_window" value="-1.0"/>
19124 <param name="mz_extraction_window" value="0.05"/> 22453 <param name="mz_extraction_window" value="0.05"/>
19125 <param name="mz_extraction_window_ms1" value="0.05"/> 22454 <param name="mz_extraction_window_ms1" value="50.0"/>
19126 <param name="im_extraction_window_ms1" value="-1.0"/> 22455 <param name="im_extraction_window_ms1" value="-1.0"/>
19127 <section name="Debugging"/> 22456 <section name="Debugging"/>
19128 <section name="Calibration"> 22457 <section name="Calibration">
19129 <param name="ms1_im_calibration" value="false"/> 22458 <param name="ms1_im_calibration" value="false"/>
19130 <param name="im_correction_function" value="linear"/> 22459 <param name="im_correction_function" value="linear"/>
19148 <param name="OverallQualityCutoff" value="5.5"/> 22477 <param name="OverallQualityCutoff" value="5.5"/>
19149 <param name="NrRTBins" value="10"/> 22478 <param name="NrRTBins" value="10"/>
19150 <param name="MinPeptidesPerBin" value="1"/> 22479 <param name="MinPeptidesPerBin" value="1"/>
19151 <param name="MinBinsFilled" value="8"/> 22480 <param name="MinBinsFilled" value="8"/>
19152 <section name="lowess"> 22481 <section name="lowess">
19153 <param name="span" value="0.666666666666667"/> 22482 <param name="span" value="0.05"/>
19154 </section> 22483 </section>
19155 <section name="b_spline"> 22484 <section name="b_spline">
19156 <param name="num_nodes" value="5"/> 22485 <param name="num_nodes" value="5"/>
19157 </section> 22486 </section>
19158 </section> 22487 </section>
19162 <param name="quantification_cutoff" value="0.0"/> 22491 <param name="quantification_cutoff" value="0.0"/>
19163 <param name="write_convex_hull" value="false"/> 22492 <param name="write_convex_hull" value="false"/>
19164 <param name="spectrum_addition_method" value="simple"/> 22493 <param name="spectrum_addition_method" value="simple"/>
19165 <param name="add_up_spectra" value="1"/> 22494 <param name="add_up_spectra" value="1"/>
19166 <param name="spacing_for_spectra_resampling" value="0.005"/> 22495 <param name="spacing_for_spectra_resampling" value="0.005"/>
19167 <param name="uis_threshold_sn" value="0"/> 22496 <param name="uis_threshold_sn" value="-1"/>
19168 <param name="uis_threshold_peak_area" value="0"/> 22497 <param name="uis_threshold_peak_area" value="0"/>
19169 <param name="scoring_model" value="default"/> 22498 <param name="scoring_model" value="default"/>
19170 <param name="im_extra_drift" value="0.0"/> 22499 <param name="im_extra_drift" value="0.0"/>
22500 <param name="strict" value="true"/>
19171 <section name="TransitionGroupPicker"> 22501 <section name="TransitionGroupPicker">
19172 <param name="stop_after_feature" value="-1"/> 22502 <param name="stop_after_feature" value="-1"/>
19173 <param name="min_peak_width" value="-1.0"/> 22503 <param name="min_peak_width" value="-1.0"/>
19174 <param name="peak_integration" value="original"/> 22504 <param name="peak_integration" value="original"/>
19175 <param name="background_subtraction" value="none"/> 22505 <param name="background_subtraction" value="none"/>
19221 <param name="use_intensity_score" value="true"/> 22551 <param name="use_intensity_score" value="true"/>
19222 <param name="use_nr_peaks_score" value="true"/> 22552 <param name="use_nr_peaks_score" value="true"/>
19223 <param name="use_total_xic_score" value="true"/> 22553 <param name="use_total_xic_score" value="true"/>
19224 <param name="use_total_mi_score" value="false"/> 22554 <param name="use_total_mi_score" value="false"/>
19225 <param name="use_sn_score" value="true"/> 22555 <param name="use_sn_score" value="true"/>
19226 <param name="use_mi_score" value="false"/> 22556 <param name="use_mi_score" value="true"/>
19227 <param name="use_dia_scores" value="true"/> 22557 <param name="use_dia_scores" value="true"/>
19228 <param name="use_ms1_correlation" value="false"/> 22558 <param name="use_ms1_correlation" value="false"/>
19229 <param name="use_sonar_scores" value="false"/> 22559 <param name="use_sonar_scores" value="false"/>
19230 <param name="use_ion_mobility_scores" value="false"/> 22560 <param name="use_ion_mobility_scores" value="false"/>
19231 <param name="use_ms1_fullscan" value="false"/> 22561 <param name="use_ms1_fullscan" value="false"/>
19232 <param name="use_ms1_mi" value="false"/> 22562 <param name="use_ms1_mi" value="false"/>
19233 <param name="use_uis_scores" value="false"/> 22563 <param name="use_uis_scores" value="false"/>
19234 </section> 22564 </section>
19235 </section> 22565 </section>
19236 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> 22566 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
19237 <output name="ctd_out" ftype="xml"> 22567 <output name="ctd_out" ftype="xml">
19238 <assert_contents> 22568 <assert_contents>
19239 <is_valid_xml/> 22569 <is_valid_xml/>
19240 </assert_contents> 22570 </assert_contents>
19241 </output> 22571 </output>
19242 </test> 22572 </test>
19243 <test expect_num_outputs="3"> 22573 <test expect_num_outputs="2">
19244 <conditional name="adv_opts_cond"> 22574 <conditional name="adv_opts_cond">
19245 <param name="adv_opts_selector" value="advanced"/> 22575 <param name="adv_opts_selector" value="advanced"/>
19246 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> 22576 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19247 <param name="sort_swath_maps" value="false"/> 22577 <param name="sort_swath_maps" value="false"/>
19248 <param name="use_ms1_traces" value="true"/> 22578 <param name="enable_ms1" value="true"/>
19249 <param name="enable_uis_scoring" value="false"/> 22579 <param name="enable_ipf" value="true"/>
19250 <param name="out_chrom_type" value="mzML"/>
19251 <param name="min_upper_edge_dist" value="0.0"/> 22580 <param name="min_upper_edge_dist" value="0.0"/>
19252 <param name="extra_rt_extraction_window" value="0.0"/> 22581 <param name="extra_rt_extraction_window" value="0.0"/>
19253 <param name="mz_extraction_window_unit" value="Th"/> 22582 <param name="mz_extraction_window_unit" value="Th"/>
19254 <param name="mz_extraction_window_ms1_unit" value="Th"/> 22583 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19255 <param name="use_ms1_ion_mobility" value="true"/> 22584 <param name="use_ms1_ion_mobility" value="true"/>
19256 <param name="matching_window_only" value="false"/> 22585 <param name="matching_window_only" value="false"/>
19257 <param name="irt_mz_extraction_window" value="0.05"/> 22586 <param name="irt_mz_extraction_window" value="50.0"/>
19258 <param name="irt_mz_extraction_window_unit" value="Th"/> 22587 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19259 <param name="irt_im_extraction_window" value="-1.0"/> 22588 <param name="irt_im_extraction_window" value="-1.0"/>
19260 <param name="min_rsq" value="0.95"/> 22589 <param name="min_rsq" value="0.95"/>
19261 <param name="min_coverage" value="0.6"/> 22590 <param name="min_coverage" value="0.6"/>
19262 <param name="split_file_input" value="false"/> 22591 <param name="split_file_input" value="false"/>
19263 <param name="use_elution_model_score" value="false"/> 22592 <param name="use_elution_model_score" value="false"/>
19264 <param name="readOptions" value="normal"/> 22593 <param name="readOptions" value="normal"/>
19265 <param name="mz_correction_function" value="none"/> 22594 <param name="mz_correction_function" value="none"/>
19266 <param name="extraction_function" value="tophat"/> 22595 <param name="extraction_function" value="tophat"/>
19267 <param name="batchSize" value="250"/> 22596 <param name="batchSize" value="1000"/>
19268 <param name="ms1_isotopes" value="0"/> 22597 <param name="ms1_isotopes" value="0"/>
19269 <param name="force" value="false"/> 22598 <param name="force" value="false"/>
19270 <param name="test" value="true"/> 22599 <param name="test" value="true"/>
19271 </conditional> 22600 </conditional>
19272 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> 22601 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19273 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 22602 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19274 <param name="tr_type" value=""/> 22603 <param name="tr_type" value=""/>
19275 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> 22604 <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19276 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19277 <param name="sonar" value="false"/> 22605 <param name="sonar" value="false"/>
19278 <param name="rt_extraction_window" value="600.0"/> 22606 <param name="rt_extraction_window" value="600.0"/>
19279 <param name="ion_mobility_window" value="-1.0"/> 22607 <param name="ion_mobility_window" value="-1.0"/>
19280 <param name="mz_extraction_window" value="0.05"/> 22608 <param name="mz_extraction_window" value="0.05"/>
19281 <param name="mz_extraction_window_ms1" value="0.05"/> 22609 <param name="mz_extraction_window_ms1" value="50.0"/>
19282 <param name="im_extraction_window_ms1" value="-1.0"/> 22610 <param name="im_extraction_window_ms1" value="-1.0"/>
19283 <section name="Debugging"/> 22611 <section name="Debugging"/>
19284 <section name="Calibration"> 22612 <section name="Calibration">
19285 <param name="ms1_im_calibration" value="false"/> 22613 <param name="ms1_im_calibration" value="false"/>
19286 <param name="im_correction_function" value="linear"/> 22614 <param name="im_correction_function" value="linear"/>
19304 <param name="OverallQualityCutoff" value="5.5"/> 22632 <param name="OverallQualityCutoff" value="5.5"/>
19305 <param name="NrRTBins" value="10"/> 22633 <param name="NrRTBins" value="10"/>
19306 <param name="MinPeptidesPerBin" value="1"/> 22634 <param name="MinPeptidesPerBin" value="1"/>
19307 <param name="MinBinsFilled" value="8"/> 22635 <param name="MinBinsFilled" value="8"/>
19308 <section name="lowess"> 22636 <section name="lowess">
19309 <param name="span" value="0.666666666666667"/> 22637 <param name="span" value="0.05"/>
19310 </section> 22638 </section>
19311 <section name="b_spline"> 22639 <section name="b_spline">
19312 <param name="num_nodes" value="5"/> 22640 <param name="num_nodes" value="5"/>
19313 </section> 22641 </section>
19314 </section> 22642 </section>
19318 <param name="quantification_cutoff" value="0.0"/> 22646 <param name="quantification_cutoff" value="0.0"/>
19319 <param name="write_convex_hull" value="false"/> 22647 <param name="write_convex_hull" value="false"/>
19320 <param name="spectrum_addition_method" value="simple"/> 22648 <param name="spectrum_addition_method" value="simple"/>
19321 <param name="add_up_spectra" value="1"/> 22649 <param name="add_up_spectra" value="1"/>
19322 <param name="spacing_for_spectra_resampling" value="0.005"/> 22650 <param name="spacing_for_spectra_resampling" value="0.005"/>
19323 <param name="uis_threshold_sn" value="0"/> 22651 <param name="uis_threshold_sn" value="-1"/>
19324 <param name="uis_threshold_peak_area" value="0"/> 22652 <param name="uis_threshold_peak_area" value="0"/>
19325 <param name="scoring_model" value="default"/> 22653 <param name="scoring_model" value="default"/>
19326 <param name="im_extra_drift" value="0.0"/> 22654 <param name="im_extra_drift" value="0.0"/>
22655 <param name="strict" value="true"/>
19327 <section name="TransitionGroupPicker"> 22656 <section name="TransitionGroupPicker">
19328 <param name="stop_after_feature" value="-1"/> 22657 <param name="stop_after_feature" value="-1"/>
19329 <param name="min_peak_width" value="-1.0"/> 22658 <param name="min_peak_width" value="-1.0"/>
19330 <param name="peak_integration" value="original"/> 22659 <param name="peak_integration" value="original"/>
19331 <param name="background_subtraction" value="none"/> 22660 <param name="background_subtraction" value="none"/>
19375 <param name="use_rt_score" value="true"/> 22704 <param name="use_rt_score" value="true"/>
19376 <param name="use_library_score" value="true"/> 22705 <param name="use_library_score" value="true"/>
19377 <param name="use_intensity_score" value="true"/> 22706 <param name="use_intensity_score" value="true"/>
19378 <param name="use_nr_peaks_score" value="true"/> 22707 <param name="use_nr_peaks_score" value="true"/>
19379 <param name="use_total_xic_score" value="true"/> 22708 <param name="use_total_xic_score" value="true"/>
19380 <param name="use_total_mi_score" value="false"/> 22709 <param name="use_total_mi_score" value="true"/>
19381 <param name="use_sn_score" value="true"/> 22710 <param name="use_sn_score" value="true"/>
19382 <param name="use_mi_score" value="false"/> 22711 <param name="use_mi_score" value="true"/>
19383 <param name="use_dia_scores" value="true"/> 22712 <param name="use_dia_scores" value="true"/>
19384 <param name="use_ms1_correlation" value="false"/> 22713 <param name="use_ms1_correlation" value="false"/>
19385 <param name="use_sonar_scores" value="false"/> 22714 <param name="use_sonar_scores" value="false"/>
19386 <param name="use_ion_mobility_scores" value="false"/> 22715 <param name="use_ion_mobility_scores" value="false"/>
19387 <param name="use_ms1_fullscan" value="false"/> 22716 <param name="use_ms1_fullscan" value="false"/>
19388 <param name="use_ms1_mi" value="false"/> 22717 <param name="use_ms1_mi" value="false"/>
19389 <param name="use_uis_scores" value="false"/> 22718 <param name="use_uis_scores" value="false"/>
19390 </section> 22719 </section>
19391 </section> 22720 </section>
19392 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> 22721 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
19393 <output name="ctd_out" ftype="xml"> 22722 <output name="ctd_out" ftype="xml">
19394 <assert_contents> 22723 <assert_contents>
19395 <is_valid_xml/> 22724 <is_valid_xml/>
19396 </assert_contents> 22725 </assert_contents>
19397 </output> 22726 </output>
19398 </test> 22727 </test>
19399 <test expect_num_outputs="3"> 22728 <test expect_num_outputs="4">
19400 <conditional name="adv_opts_cond"> 22729 <conditional name="adv_opts_cond">
19401 <param name="adv_opts_selector" value="advanced"/> 22730 <param name="adv_opts_selector" value="advanced"/>
19402 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19403 <param name="sort_swath_maps" value="false"/> 22731 <param name="sort_swath_maps" value="false"/>
19404 <param name="use_ms1_traces" value="true"/> 22732 <param name="enable_ms1" value="true"/>
19405 <param name="enable_uis_scoring" value="false"/> 22733 <param name="enable_ipf" value="true"/>
19406 <param name="out_chrom_type" value="mzML"/> 22734 <param name="out_chrom_type" value="mzML"/>
19407 <param name="min_upper_edge_dist" value="0.0"/> 22735 <param name="min_upper_edge_dist" value="0.0"/>
19408 <param name="extra_rt_extraction_window" value="0.0"/> 22736 <param name="extra_rt_extraction_window" value="0.0"/>
19409 <param name="mz_extraction_window_unit" value="Th"/> 22737 <param name="mz_extraction_window_unit" value="Th"/>
19410 <param name="mz_extraction_window_ms1_unit" value="Th"/> 22738 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19411 <param name="use_ms1_ion_mobility" value="true"/> 22739 <param name="use_ms1_ion_mobility" value="true"/>
19412 <param name="matching_window_only" value="false"/> 22740 <param name="matching_window_only" value="false"/>
19413 <param name="irt_mz_extraction_window" value="0.05"/> 22741 <param name="irt_mz_extraction_window" value="50.0"/>
19414 <param name="irt_mz_extraction_window_unit" value="Th"/> 22742 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19415 <param name="irt_im_extraction_window" value="-1.0"/> 22743 <param name="irt_im_extraction_window" value="-1.0"/>
19416 <param name="min_rsq" value="0.95"/> 22744 <param name="min_rsq" value="0.95"/>
19417 <param name="min_coverage" value="0.6"/> 22745 <param name="min_coverage" value="0.6"/>
19418 <param name="split_file_input" value="false"/> 22746 <param name="split_file_input" value="false"/>
19419 <param name="use_elution_model_score" value="false"/> 22747 <param name="use_elution_model_score" value="false"/>
19420 <param name="readOptions" value="normal"/> 22748 <param name="readOptions" value="normal"/>
19421 <param name="mz_correction_function" value="none"/> 22749 <param name="mz_correction_function" value="none"/>
19422 <param name="extraction_function" value="tophat"/> 22750 <param name="extraction_function" value="tophat"/>
19423 <param name="batchSize" value="250"/> 22751 <param name="batchSize" value="1000"/>
19424 <param name="ms1_isotopes" value="0"/> 22752 <param name="ms1_isotopes" value="0"/>
19425 <param name="force" value="false"/> 22753 <param name="force" value="false"/>
19426 <param name="test" value="true"/> 22754 <param name="test" value="true"/>
19427 </conditional> 22755 </conditional>
19428 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> 22756 <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
19429 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 22757 <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
19430 <param name="tr_type" value=""/> 22758 <param name="tr_type" value=""/>
19431 <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> 22759 <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
19432 <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> 22760 <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22761 <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19433 <param name="sonar" value="false"/> 22762 <param name="sonar" value="false"/>
19434 <param name="rt_extraction_window" value="600.0"/> 22763 <param name="rt_extraction_window" value="600.0"/>
19435 <param name="ion_mobility_window" value="-1.0"/> 22764 <param name="ion_mobility_window" value="-1.0"/>
19436 <param name="mz_extraction_window" value="0.05"/> 22765 <param name="mz_extraction_window" value="0.05"/>
19437 <param name="mz_extraction_window_ms1" value="0.05"/> 22766 <param name="mz_extraction_window_ms1" value="50.0"/>
19438 <param name="im_extraction_window_ms1" value="-1.0"/> 22767 <param name="im_extraction_window_ms1" value="-1.0"/>
19439 <section name="Debugging"/> 22768 <section name="Debugging"/>
22769 <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
19440 <section name="Calibration"> 22770 <section name="Calibration">
19441 <param name="ms1_im_calibration" value="false"/> 22771 <param name="ms1_im_calibration" value="false"/>
19442 <param name="im_correction_function" value="linear"/> 22772 <param name="im_correction_function" value="linear"/>
19443 <param name="debug_im_file" value=""/> 22773 <param name="debug_im_file" value=""/>
19444 <param name="debug_mz_file" value=""/> 22774 <param name="debug_mz_file" value=""/>
19460 <param name="OverallQualityCutoff" value="5.5"/> 22790 <param name="OverallQualityCutoff" value="5.5"/>
19461 <param name="NrRTBins" value="10"/> 22791 <param name="NrRTBins" value="10"/>
19462 <param name="MinPeptidesPerBin" value="1"/> 22792 <param name="MinPeptidesPerBin" value="1"/>
19463 <param name="MinBinsFilled" value="8"/> 22793 <param name="MinBinsFilled" value="8"/>
19464 <section name="lowess"> 22794 <section name="lowess">
19465 <param name="span" value="0.666666666666667"/> 22795 <param name="span" value="0.6666666666666666"/>
19466 </section> 22796 </section>
19467 <section name="b_spline"> 22797 <section name="b_spline">
19468 <param name="num_nodes" value="5"/> 22798 <param name="num_nodes" value="5"/>
19469 </section> 22799 </section>
19470 </section> 22800 </section>
19474 <param name="quantification_cutoff" value="0.0"/> 22804 <param name="quantification_cutoff" value="0.0"/>
19475 <param name="write_convex_hull" value="false"/> 22805 <param name="write_convex_hull" value="false"/>
19476 <param name="spectrum_addition_method" value="simple"/> 22806 <param name="spectrum_addition_method" value="simple"/>
19477 <param name="add_up_spectra" value="1"/> 22807 <param name="add_up_spectra" value="1"/>
19478 <param name="spacing_for_spectra_resampling" value="0.005"/> 22808 <param name="spacing_for_spectra_resampling" value="0.005"/>
19479 <param name="uis_threshold_sn" value="0"/> 22809 <param name="uis_threshold_sn" value="-1"/>
19480 <param name="uis_threshold_peak_area" value="0"/> 22810 <param name="uis_threshold_peak_area" value="0"/>
19481 <param name="scoring_model" value="default"/> 22811 <param name="scoring_model" value="default"/>
19482 <param name="im_extra_drift" value="0.0"/> 22812 <param name="im_extra_drift" value="0.0"/>
22813 <param name="strict" value="true"/>
19483 <section name="TransitionGroupPicker"> 22814 <section name="TransitionGroupPicker">
19484 <param name="stop_after_feature" value="-1"/> 22815 <param name="stop_after_feature" value="-1"/>
19485 <param name="min_peak_width" value="-1.0"/> 22816 <param name="min_peak_width" value="-1.0"/>
19486 <param name="peak_integration" value="original"/> 22817 <param name="peak_integration" value="original"/>
19487 <param name="background_subtraction" value="none"/> 22818 <param name="background_subtraction" value="none"/>
19531 <param name="use_rt_score" value="true"/> 22862 <param name="use_rt_score" value="true"/>
19532 <param name="use_library_score" value="true"/> 22863 <param name="use_library_score" value="true"/>
19533 <param name="use_intensity_score" value="true"/> 22864 <param name="use_intensity_score" value="true"/>
19534 <param name="use_nr_peaks_score" value="true"/> 22865 <param name="use_nr_peaks_score" value="true"/>
19535 <param name="use_total_xic_score" value="true"/> 22866 <param name="use_total_xic_score" value="true"/>
19536 <param name="use_total_mi_score" value="false"/> 22867 <param name="use_total_mi_score" value="true"/>
19537 <param name="use_sn_score" value="true"/> 22868 <param name="use_sn_score" value="true"/>
19538 <param name="use_mi_score" value="false"/> 22869 <param name="use_mi_score" value="true"/>
19539 <param name="use_dia_scores" value="true"/> 22870 <param name="use_dia_scores" value="true"/>
19540 <param name="use_ms1_correlation" value="false"/> 22871 <param name="use_ms1_correlation" value="false"/>
19541 <param name="use_sonar_scores" value="false"/> 22872 <param name="use_sonar_scores" value="false"/>
19542 <param name="use_ion_mobility_scores" value="false"/> 22873 <param name="use_ion_mobility_scores" value="false"/>
19543 <param name="use_ms1_fullscan" value="false"/> 22874 <param name="use_ms1_fullscan" value="false"/>
19544 <param name="use_ms1_mi" value="false"/> 22875 <param name="use_ms1_mi" value="false"/>
19545 <param name="use_uis_scores" value="false"/> 22876 <param name="use_uis_scores" value="false"/>
19546 </section> 22877 </section>
19547 </section> 22878 </section>
19548 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> 22879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
19549 <output name="ctd_out" ftype="xml"> 22880 <output name="ctd_out" ftype="xml">
19550 <assert_contents> 22881 <assert_contents>
19551 <is_valid_xml/> 22882 <is_valid_xml/>
19552 </assert_contents> 22883 </assert_contents>
19553 </output> 22884 </output>
19554 </test> 22885 </test>
19555 <test expect_num_outputs="3"> 22886 <test expect_num_outputs="3">
19556 <conditional name="adv_opts_cond"> 22887 <conditional name="adv_opts_cond">
19557 <param name="adv_opts_selector" value="advanced"/> 22888 <param name="adv_opts_selector" value="advanced"/>
19558 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19559 <param name="sort_swath_maps" value="false"/> 22889 <param name="sort_swath_maps" value="false"/>
19560 <param name="use_ms1_traces" value="true"/> 22890 <param name="enable_ms1" value="true"/>
19561 <param name="enable_uis_scoring" value="false"/> 22891 <param name="enable_ipf" value="true"/>
19562 <param name="out_chrom_type" value="mzML"/> 22892 <param name="out_chrom_type" value="mzML"/>
19563 <param name="min_upper_edge_dist" value="0.0"/> 22893 <param name="min_upper_edge_dist" value="0.0"/>
19564 <param name="extra_rt_extraction_window" value="0.0"/> 22894 <param name="extra_rt_extraction_window" value="0.0"/>
19565 <param name="mz_extraction_window_unit" value="Th"/> 22895 <param name="mz_extraction_window_unit" value="ppm"/>
19566 <param name="mz_extraction_window_ms1_unit" value="Th"/> 22896 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
19567 <param name="use_ms1_ion_mobility" value="true"/> 22897 <param name="use_ms1_ion_mobility" value="true"/>
19568 <param name="matching_window_only" value="false"/> 22898 <param name="matching_window_only" value="true"/>
19569 <param name="irt_mz_extraction_window" value="0.05"/> 22899 <param name="irt_mz_extraction_window" value="50.0"/>
19570 <param name="irt_mz_extraction_window_unit" value="Th"/> 22900 <param name="irt_mz_extraction_window_unit" value="ppm"/>
19571 <param name="irt_im_extraction_window" value="-1.0"/> 22901 <param name="irt_im_extraction_window" value="-1.0"/>
19572 <param name="min_rsq" value="0.95"/> 22902 <param name="min_rsq" value="0.95"/>
19573 <param name="min_coverage" value="0.6"/> 22903 <param name="min_coverage" value="0.6"/>
19574 <param name="split_file_input" value="false"/> 22904 <param name="split_file_input" value="false"/>
19575 <param name="use_elution_model_score" value="false"/> 22905 <param name="use_elution_model_score" value="false"/>
19576 <param name="readOptions" value="cache"/> 22906 <param name="readOptions" value="workingInMemory"/>
19577 <param name="mz_correction_function" value="none"/> 22907 <param name="mz_correction_function" value="none"/>
19578 <param name="extraction_function" value="tophat"/> 22908 <param name="extraction_function" value="tophat"/>
19579 <param name="batchSize" value="250"/> 22909 <param name="batchSize" value="1000"/>
19580 <param name="ms1_isotopes" value="0"/> 22910 <param name="ms1_isotopes" value="3"/>
19581 <param name="force" value="false"/> 22911 <param name="force" value="false"/>
19582 <param name="test" value="true"/> 22912 <param name="test" value="false"/>
19583 </conditional> 22913 </conditional>
19584 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> 22914 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
19585 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 22915 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
19586 <param name="tr_type" value=""/> 22916 <param name="tr_type" value=""/>
19587 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> 22917 <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19588 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 22918 <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19589 <param name="sonar" value="false"/> 22919 <param name="sonar" value="false"/>
19590 <param name="rt_extraction_window" value="600.0"/> 22920 <param name="rt_extraction_window" value="600.0"/>
19591 <param name="ion_mobility_window" value="-1.0"/> 22921 <param name="ion_mobility_window" value="-1.0"/>
19592 <param name="mz_extraction_window" value="0.05"/> 22922 <param name="mz_extraction_window" value="50.0"/>
19593 <param name="mz_extraction_window_ms1" value="0.05"/> 22923 <param name="mz_extraction_window_ms1" value="50.0"/>
19594 <param name="im_extraction_window_ms1" value="-1.0"/> 22924 <param name="im_extraction_window_ms1" value="-1.0"/>
19595 <section name="Debugging"/> 22925 <section name="Debugging"/>
19596 <section name="Calibration"> 22926 <section name="Calibration">
19597 <param name="ms1_im_calibration" value="false"/> 22927 <param name="ms1_im_calibration" value="false"/>
19598 <param name="im_correction_function" value="linear"/> 22928 <param name="im_correction_function" value="linear"/>
19616 <param name="OverallQualityCutoff" value="5.5"/> 22946 <param name="OverallQualityCutoff" value="5.5"/>
19617 <param name="NrRTBins" value="10"/> 22947 <param name="NrRTBins" value="10"/>
19618 <param name="MinPeptidesPerBin" value="1"/> 22948 <param name="MinPeptidesPerBin" value="1"/>
19619 <param name="MinBinsFilled" value="8"/> 22949 <param name="MinBinsFilled" value="8"/>
19620 <section name="lowess"> 22950 <section name="lowess">
19621 <param name="span" value="0.666666666666667"/> 22951 <param name="span" value="0.05"/>
19622 </section> 22952 </section>
19623 <section name="b_spline"> 22953 <section name="b_spline">
19624 <param name="num_nodes" value="5"/> 22954 <param name="num_nodes" value="5"/>
19625 </section> 22955 </section>
19626 </section> 22956 </section>
19630 <param name="quantification_cutoff" value="0.0"/> 22960 <param name="quantification_cutoff" value="0.0"/>
19631 <param name="write_convex_hull" value="false"/> 22961 <param name="write_convex_hull" value="false"/>
19632 <param name="spectrum_addition_method" value="simple"/> 22962 <param name="spectrum_addition_method" value="simple"/>
19633 <param name="add_up_spectra" value="1"/> 22963 <param name="add_up_spectra" value="1"/>
19634 <param name="spacing_for_spectra_resampling" value="0.005"/> 22964 <param name="spacing_for_spectra_resampling" value="0.005"/>
19635 <param name="uis_threshold_sn" value="0"/> 22965 <param name="uis_threshold_sn" value="-1"/>
19636 <param name="uis_threshold_peak_area" value="0"/> 22966 <param name="uis_threshold_peak_area" value="0"/>
19637 <param name="scoring_model" value="default"/> 22967 <param name="scoring_model" value="default"/>
19638 <param name="im_extra_drift" value="0.0"/> 22968 <param name="im_extra_drift" value="0.0"/>
22969 <param name="strict" value="true"/>
19639 <section name="TransitionGroupPicker"> 22970 <section name="TransitionGroupPicker">
19640 <param name="stop_after_feature" value="-1"/> 22971 <param name="stop_after_feature" value="-1"/>
19641 <param name="min_peak_width" value="-1.0"/> 22972 <param name="min_peak_width" value="-1.0"/>
19642 <param name="peak_integration" value="original"/> 22973 <param name="peak_integration" value="original"/>
19643 <param name="background_subtraction" value="none"/> 22974 <param name="background_subtraction" value="none"/>
19644 <param name="recalculate_peaks" value="true"/> 22975 <param name="recalculate_peaks" value="true"/>
19645 <param name="use_precursors" value="false"/> 22976 <param name="use_precursors" value="false"/>
19646 <param name="use_consensus" value="true"/>
19647 <param name="recalculate_peaks_max_z" value="0.75"/>
19648 <param name="minimal_quality" value="-1.5"/>
19649 <param name="resample_boundary" value="15.0"/>
19650 <param name="compute_peak_quality" value="true"/>
19651 <param name="compute_peak_shape_metrics" value="false"/>
19652 <param name="compute_total_mi" value="false"/>
19653 <param name="boundary_selection_method" value="largest"/>
19654 <section name="PeakPickerMRM">
19655 <param name="sgolay_frame_length" value="11"/>
19656 <param name="sgolay_polynomial_order" value="3"/>
19657 <param name="gauss_width" value="30.0"/>
19658 <param name="use_gauss" value="false"/>
19659 <param name="peak_width" value="-1.0"/>
19660 <param name="signal_to_noise" value="0.1"/>
19661 <param name="write_sn_log_messages" value="false"/>
19662 <param name="remove_overlapping_peaks" value="true"/>
19663 <param name="method" value="corrected"/>
19664 </section>
19665 <section name="PeakIntegrator">
19666 <param name="integration_type" value="intensity_sum"/>
19667 <param name="baseline_type" value="base_to_base"/>
19668 <param name="fit_EMG" value="false"/>
19669 </section>
19670 </section>
19671 <section name="DIAScoring">
19672 <param name="dia_extraction_window" value="0.05"/>
19673 <param name="dia_extraction_unit" value="Th"/>
19674 <param name="dia_centroided" value="false"/>
19675 <param name="dia_byseries_intensity_min" value="300.0"/>
19676 <param name="dia_byseries_ppm_diff" value="10.0"/>
19677 <param name="dia_nr_isotopes" value="4"/>
19678 <param name="dia_nr_charges" value="4"/>
19679 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19680 </section>
19681 <section name="EMGScoring">
19682 <param name="max_iteration" value="10"/>
19683 </section>
19684 <section name="Scores">
19685 <param name="use_shape_score" value="true"/>
19686 <param name="use_coelution_score" value="true"/>
19687 <param name="use_rt_score" value="true"/>
19688 <param name="use_library_score" value="true"/>
19689 <param name="use_intensity_score" value="true"/>
19690 <param name="use_nr_peaks_score" value="true"/>
19691 <param name="use_total_xic_score" value="true"/>
19692 <param name="use_total_mi_score" value="false"/>
19693 <param name="use_sn_score" value="true"/>
19694 <param name="use_mi_score" value="false"/>
19695 <param name="use_dia_scores" value="true"/>
19696 <param name="use_ms1_correlation" value="false"/>
19697 <param name="use_sonar_scores" value="false"/>
19698 <param name="use_ion_mobility_scores" value="false"/>
19699 <param name="use_ms1_fullscan" value="false"/>
19700 <param name="use_ms1_mi" value="false"/>
19701 <param name="use_uis_scores" value="false"/>
19702 </section>
19703 </section>
19704 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19705 <output name="ctd_out" ftype="xml">
19706 <assert_contents>
19707 <is_valid_xml/>
19708 </assert_contents>
19709 </output>
19710 </test>
19711 <test expect_num_outputs="3">
19712 <conditional name="adv_opts_cond">
19713 <param name="adv_opts_selector" value="advanced"/>
19714 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19715 <param name="sort_swath_maps" value="false"/>
19716 <param name="use_ms1_traces" value="true"/>
19717 <param name="enable_uis_scoring" value="false"/>
19718 <param name="out_chrom_type" value="mzML"/>
19719 <param name="min_upper_edge_dist" value="0.0"/>
19720 <param name="extra_rt_extraction_window" value="0.0"/>
19721 <param name="mz_extraction_window_unit" value="Th"/>
19722 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19723 <param name="use_ms1_ion_mobility" value="true"/>
19724 <param name="matching_window_only" value="false"/>
19725 <param name="irt_mz_extraction_window" value="0.05"/>
19726 <param name="irt_mz_extraction_window_unit" value="Th"/>
19727 <param name="irt_im_extraction_window" value="-1.0"/>
19728 <param name="min_rsq" value="0.95"/>
19729 <param name="min_coverage" value="0.6"/>
19730 <param name="split_file_input" value="false"/>
19731 <param name="use_elution_model_score" value="false"/>
19732 <param name="readOptions" value="cacheWorkingInMemory"/>
19733 <param name="mz_correction_function" value="none"/>
19734 <param name="extraction_function" value="tophat"/>
19735 <param name="batchSize" value="250"/>
19736 <param name="ms1_isotopes" value="0"/>
19737 <param name="force" value="false"/>
19738 <param name="test" value="true"/>
19739 </conditional>
19740 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19741 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19742 <param name="tr_type" value=""/>
19743 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19744 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19745 <param name="sonar" value="false"/>
19746 <param name="rt_extraction_window" value="600.0"/>
19747 <param name="ion_mobility_window" value="-1.0"/>
19748 <param name="mz_extraction_window" value="0.05"/>
19749 <param name="mz_extraction_window_ms1" value="0.05"/>
19750 <param name="im_extraction_window_ms1" value="-1.0"/>
19751 <section name="Debugging"/>
19752 <section name="Calibration">
19753 <param name="ms1_im_calibration" value="false"/>
19754 <param name="im_correction_function" value="linear"/>
19755 <param name="debug_im_file" value=""/>
19756 <param name="debug_mz_file" value=""/>
19757 </section>
19758 <section name="Library">
19759 <param name="retentionTimeInterpretation" value="iRT"/>
19760 <param name="override_group_label_check" value="false"/>
19761 <param name="force_invalid_mods" value="false"/>
19762 </section>
19763 <section name="RTNormalization">
19764 <param name="alignmentMethod" value="linear"/>
19765 <param name="outlierMethod" value="iter_residual"/>
19766 <param name="useIterativeChauvenet" value="false"/>
19767 <param name="RANSACMaxIterations" value="1000"/>
19768 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19769 <param name="RANSACSamplingSize" value="10"/>
19770 <param name="estimateBestPeptides" value="false"/>
19771 <param name="InitialQualityCutoff" value="0.5"/>
19772 <param name="OverallQualityCutoff" value="5.5"/>
19773 <param name="NrRTBins" value="10"/>
19774 <param name="MinPeptidesPerBin" value="1"/>
19775 <param name="MinBinsFilled" value="8"/>
19776 <section name="lowess">
19777 <param name="span" value="0.666666666666667"/>
19778 </section>
19779 <section name="b_spline">
19780 <param name="num_nodes" value="5"/>
19781 </section>
19782 </section>
19783 <section name="Scoring">
19784 <param name="stop_report_after_feature" value="5"/>
19785 <param name="rt_normalization_factor" value="100.0"/>
19786 <param name="quantification_cutoff" value="0.0"/>
19787 <param name="write_convex_hull" value="false"/>
19788 <param name="spectrum_addition_method" value="simple"/>
19789 <param name="add_up_spectra" value="1"/>
19790 <param name="spacing_for_spectra_resampling" value="0.005"/>
19791 <param name="uis_threshold_sn" value="0"/>
19792 <param name="uis_threshold_peak_area" value="0"/>
19793 <param name="scoring_model" value="default"/>
19794 <param name="im_extra_drift" value="0.0"/>
19795 <section name="TransitionGroupPicker">
19796 <param name="stop_after_feature" value="-1"/>
19797 <param name="min_peak_width" value="-1.0"/>
19798 <param name="peak_integration" value="original"/>
19799 <param name="background_subtraction" value="none"/>
19800 <param name="recalculate_peaks" value="true"/>
19801 <param name="use_precursors" value="false"/>
19802 <param name="use_consensus" value="true"/>
19803 <param name="recalculate_peaks_max_z" value="0.75"/>
19804 <param name="minimal_quality" value="-1.5"/>
19805 <param name="resample_boundary" value="15.0"/>
19806 <param name="compute_peak_quality" value="true"/>
19807 <param name="compute_peak_shape_metrics" value="false"/>
19808 <param name="compute_total_mi" value="false"/>
19809 <param name="boundary_selection_method" value="largest"/>
19810 <section name="PeakPickerMRM">
19811 <param name="sgolay_frame_length" value="11"/>
19812 <param name="sgolay_polynomial_order" value="3"/>
19813 <param name="gauss_width" value="30.0"/>
19814 <param name="use_gauss" value="false"/>
19815 <param name="peak_width" value="-1.0"/>
19816 <param name="signal_to_noise" value="0.1"/>
19817 <param name="write_sn_log_messages" value="false"/>
19818 <param name="remove_overlapping_peaks" value="true"/>
19819 <param name="method" value="corrected"/>
19820 </section>
19821 <section name="PeakIntegrator">
19822 <param name="integration_type" value="intensity_sum"/>
19823 <param name="baseline_type" value="base_to_base"/>
19824 <param name="fit_EMG" value="false"/>
19825 </section>
19826 </section>
19827 <section name="DIAScoring">
19828 <param name="dia_extraction_window" value="0.05"/>
19829 <param name="dia_extraction_unit" value="Th"/>
19830 <param name="dia_centroided" value="false"/>
19831 <param name="dia_byseries_intensity_min" value="300.0"/>
19832 <param name="dia_byseries_ppm_diff" value="10.0"/>
19833 <param name="dia_nr_isotopes" value="4"/>
19834 <param name="dia_nr_charges" value="4"/>
19835 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19836 </section>
19837 <section name="EMGScoring">
19838 <param name="max_iteration" value="10"/>
19839 </section>
19840 <section name="Scores">
19841 <param name="use_shape_score" value="true"/>
19842 <param name="use_coelution_score" value="true"/>
19843 <param name="use_rt_score" value="true"/>
19844 <param name="use_library_score" value="true"/>
19845 <param name="use_intensity_score" value="true"/>
19846 <param name="use_nr_peaks_score" value="true"/>
19847 <param name="use_total_xic_score" value="true"/>
19848 <param name="use_total_mi_score" value="false"/>
19849 <param name="use_sn_score" value="true"/>
19850 <param name="use_mi_score" value="false"/>
19851 <param name="use_dia_scores" value="true"/>
19852 <param name="use_ms1_correlation" value="false"/>
19853 <param name="use_sonar_scores" value="false"/>
19854 <param name="use_ion_mobility_scores" value="false"/>
19855 <param name="use_ms1_fullscan" value="false"/>
19856 <param name="use_ms1_mi" value="false"/>
19857 <param name="use_uis_scores" value="false"/>
19858 </section>
19859 </section>
19860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19861 <output name="ctd_out" ftype="xml">
19862 <assert_contents>
19863 <is_valid_xml/>
19864 </assert_contents>
19865 </output>
19866 </test>
19867 <test expect_num_outputs="3">
19868 <conditional name="adv_opts_cond">
19869 <param name="adv_opts_selector" value="advanced"/>
19870 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19871 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
19872 <param name="sort_swath_maps" value="false"/>
19873 <param name="use_ms1_traces" value="true"/>
19874 <param name="enable_uis_scoring" value="false"/>
19875 <param name="out_chrom_type" value="mzML"/>
19876 <param name="min_upper_edge_dist" value="0.0"/>
19877 <param name="extra_rt_extraction_window" value="0.0"/>
19878 <param name="mz_extraction_window_unit" value="Th"/>
19879 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19880 <param name="use_ms1_ion_mobility" value="true"/>
19881 <param name="matching_window_only" value="false"/>
19882 <param name="irt_mz_extraction_window" value="0.05"/>
19883 <param name="irt_mz_extraction_window_unit" value="Th"/>
19884 <param name="irt_im_extraction_window" value="-1.0"/>
19885 <param name="min_rsq" value="0.95"/>
19886 <param name="min_coverage" value="0.6"/>
19887 <param name="split_file_input" value="false"/>
19888 <param name="use_elution_model_score" value="false"/>
19889 <param name="readOptions" value="normal"/>
19890 <param name="mz_correction_function" value="none"/>
19891 <param name="extraction_function" value="tophat"/>
19892 <param name="batchSize" value="250"/>
19893 <param name="ms1_isotopes" value="0"/>
19894 <param name="force" value="false"/>
19895 <param name="test" value="true"/>
19896 </conditional>
19897 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19898 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19899 <param name="tr_type" value=""/>
19900 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19901 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19902 <param name="sonar" value="false"/>
19903 <param name="rt_extraction_window" value="600.0"/>
19904 <param name="ion_mobility_window" value="-1.0"/>
19905 <param name="mz_extraction_window" value="0.05"/>
19906 <param name="mz_extraction_window_ms1" value="0.05"/>
19907 <param name="im_extraction_window_ms1" value="-1.0"/>
19908 <section name="Debugging"/>
19909 <section name="Calibration">
19910 <param name="ms1_im_calibration" value="false"/>
19911 <param name="im_correction_function" value="linear"/>
19912 <param name="debug_im_file" value=""/>
19913 <param name="debug_mz_file" value=""/>
19914 </section>
19915 <section name="Library">
19916 <param name="retentionTimeInterpretation" value="iRT"/>
19917 <param name="override_group_label_check" value="false"/>
19918 <param name="force_invalid_mods" value="false"/>
19919 </section>
19920 <section name="RTNormalization">
19921 <param name="alignmentMethod" value="linear"/>
19922 <param name="outlierMethod" value="iter_residual"/>
19923 <param name="useIterativeChauvenet" value="false"/>
19924 <param name="RANSACMaxIterations" value="1000"/>
19925 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19926 <param name="RANSACSamplingSize" value="10"/>
19927 <param name="estimateBestPeptides" value="false"/>
19928 <param name="InitialQualityCutoff" value="0.5"/>
19929 <param name="OverallQualityCutoff" value="5.5"/>
19930 <param name="NrRTBins" value="10"/>
19931 <param name="MinPeptidesPerBin" value="1"/>
19932 <param name="MinBinsFilled" value="8"/>
19933 <section name="lowess">
19934 <param name="span" value="0.666666666666667"/>
19935 </section>
19936 <section name="b_spline">
19937 <param name="num_nodes" value="5"/>
19938 </section>
19939 </section>
19940 <section name="Scoring">
19941 <param name="stop_report_after_feature" value="5"/>
19942 <param name="rt_normalization_factor" value="100.0"/>
19943 <param name="quantification_cutoff" value="0.0"/>
19944 <param name="write_convex_hull" value="false"/>
19945 <param name="spectrum_addition_method" value="simple"/>
19946 <param name="add_up_spectra" value="1"/>
19947 <param name="spacing_for_spectra_resampling" value="0.005"/>
19948 <param name="uis_threshold_sn" value="0"/>
19949 <param name="uis_threshold_peak_area" value="0"/>
19950 <param name="scoring_model" value="default"/>
19951 <param name="im_extra_drift" value="0.0"/>
19952 <section name="TransitionGroupPicker">
19953 <param name="stop_after_feature" value="-1"/>
19954 <param name="min_peak_width" value="-1.0"/>
19955 <param name="peak_integration" value="original"/>
19956 <param name="background_subtraction" value="none"/>
19957 <param name="recalculate_peaks" value="true"/>
19958 <param name="use_precursors" value="false"/>
19959 <param name="use_consensus" value="true"/>
19960 <param name="recalculate_peaks_max_z" value="0.75"/>
19961 <param name="minimal_quality" value="-1.5"/>
19962 <param name="resample_boundary" value="15.0"/>
19963 <param name="compute_peak_quality" value="true"/>
19964 <param name="compute_peak_shape_metrics" value="false"/>
19965 <param name="compute_total_mi" value="false"/>
19966 <param name="boundary_selection_method" value="largest"/>
19967 <section name="PeakPickerMRM">
19968 <param name="sgolay_frame_length" value="11"/>
19969 <param name="sgolay_polynomial_order" value="3"/>
19970 <param name="gauss_width" value="30.0"/>
19971 <param name="use_gauss" value="false"/>
19972 <param name="peak_width" value="-1.0"/>
19973 <param name="signal_to_noise" value="0.1"/>
19974 <param name="write_sn_log_messages" value="false"/>
19975 <param name="remove_overlapping_peaks" value="true"/>
19976 <param name="method" value="corrected"/>
19977 </section>
19978 <section name="PeakIntegrator">
19979 <param name="integration_type" value="intensity_sum"/>
19980 <param name="baseline_type" value="base_to_base"/>
19981 <param name="fit_EMG" value="false"/>
19982 </section>
19983 </section>
19984 <section name="DIAScoring">
19985 <param name="dia_extraction_window" value="0.05"/>
19986 <param name="dia_extraction_unit" value="Th"/>
19987 <param name="dia_centroided" value="false"/>
19988 <param name="dia_byseries_intensity_min" value="300.0"/>
19989 <param name="dia_byseries_ppm_diff" value="10.0"/>
19990 <param name="dia_nr_isotopes" value="4"/>
19991 <param name="dia_nr_charges" value="4"/>
19992 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19993 </section>
19994 <section name="EMGScoring">
19995 <param name="max_iteration" value="10"/>
19996 </section>
19997 <section name="Scores">
19998 <param name="use_shape_score" value="true"/>
19999 <param name="use_coelution_score" value="true"/>
20000 <param name="use_rt_score" value="true"/>
20001 <param name="use_library_score" value="true"/>
20002 <param name="use_intensity_score" value="true"/>
20003 <param name="use_nr_peaks_score" value="true"/>
20004 <param name="use_total_xic_score" value="true"/>
20005 <param name="use_total_mi_score" value="false"/>
20006 <param name="use_sn_score" value="true"/>
20007 <param name="use_mi_score" value="false"/>
20008 <param name="use_dia_scores" value="true"/>
20009 <param name="use_ms1_correlation" value="false"/>
20010 <param name="use_sonar_scores" value="false"/>
20011 <param name="use_ion_mobility_scores" value="false"/>
20012 <param name="use_ms1_fullscan" value="false"/>
20013 <param name="use_ms1_mi" value="false"/>
20014 <param name="use_uis_scores" value="false"/>
20015 </section>
20016 </section>
20017 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20018 <output name="ctd_out" ftype="xml">
20019 <assert_contents>
20020 <is_valid_xml/>
20021 </assert_contents>
20022 </output>
20023 </test>
20024 <test expect_num_outputs="3">
20025 <conditional name="adv_opts_cond">
20026 <param name="adv_opts_selector" value="advanced"/>
20027 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20028 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
20029 <param name="sort_swath_maps" value="false"/>
20030 <param name="use_ms1_traces" value="true"/>
20031 <param name="enable_uis_scoring" value="false"/>
20032 <param name="out_chrom_type" value="mzML"/>
20033 <param name="min_upper_edge_dist" value="0.0"/>
20034 <param name="extra_rt_extraction_window" value="0.0"/>
20035 <param name="mz_extraction_window_unit" value="Th"/>
20036 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20037 <param name="use_ms1_ion_mobility" value="true"/>
20038 <param name="matching_window_only" value="false"/>
20039 <param name="irt_mz_extraction_window" value="0.05"/>
20040 <param name="irt_mz_extraction_window_unit" value="Th"/>
20041 <param name="irt_im_extraction_window" value="-1.0"/>
20042 <param name="min_rsq" value="0.95"/>
20043 <param name="min_coverage" value="0.6"/>
20044 <param name="split_file_input" value="false"/>
20045 <param name="use_elution_model_score" value="false"/>
20046 <param name="readOptions" value="normal"/>
20047 <param name="mz_correction_function" value="none"/>
20048 <param name="extraction_function" value="tophat"/>
20049 <param name="batchSize" value="250"/>
20050 <param name="ms1_isotopes" value="0"/>
20051 <param name="force" value="true"/>
20052 <param name="test" value="true"/>
20053 </conditional>
20054 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20055 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20056 <param name="tr_type" value=""/>
20057 <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20058 <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20059 <param name="sonar" value="false"/>
20060 <param name="rt_extraction_window" value="600.0"/>
20061 <param name="ion_mobility_window" value="-1.0"/>
20062 <param name="mz_extraction_window" value="0.05"/>
20063 <param name="mz_extraction_window_ms1" value="0.05"/>
20064 <param name="im_extraction_window_ms1" value="-1.0"/>
20065 <section name="Debugging"/>
20066 <section name="Calibration">
20067 <param name="ms1_im_calibration" value="false"/>
20068 <param name="im_correction_function" value="linear"/>
20069 <param name="debug_im_file" value=""/>
20070 <param name="debug_mz_file" value=""/>
20071 </section>
20072 <section name="Library">
20073 <param name="retentionTimeInterpretation" value="iRT"/>
20074 <param name="override_group_label_check" value="false"/>
20075 <param name="force_invalid_mods" value="false"/>
20076 </section>
20077 <section name="RTNormalization">
20078 <param name="alignmentMethod" value="linear"/>
20079 <param name="outlierMethod" value="iter_residual"/>
20080 <param name="useIterativeChauvenet" value="false"/>
20081 <param name="RANSACMaxIterations" value="1000"/>
20082 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20083 <param name="RANSACSamplingSize" value="10"/>
20084 <param name="estimateBestPeptides" value="false"/>
20085 <param name="InitialQualityCutoff" value="0.5"/>
20086 <param name="OverallQualityCutoff" value="5.5"/>
20087 <param name="NrRTBins" value="10"/>
20088 <param name="MinPeptidesPerBin" value="1"/>
20089 <param name="MinBinsFilled" value="8"/>
20090 <section name="lowess">
20091 <param name="span" value="0.666666666666667"/>
20092 </section>
20093 <section name="b_spline">
20094 <param name="num_nodes" value="5"/>
20095 </section>
20096 </section>
20097 <section name="Scoring">
20098 <param name="stop_report_after_feature" value="5"/>
20099 <param name="rt_normalization_factor" value="100.0"/>
20100 <param name="quantification_cutoff" value="0.0"/>
20101 <param name="write_convex_hull" value="false"/>
20102 <param name="spectrum_addition_method" value="simple"/>
20103 <param name="add_up_spectra" value="1"/>
20104 <param name="spacing_for_spectra_resampling" value="0.005"/>
20105 <param name="uis_threshold_sn" value="0"/>
20106 <param name="uis_threshold_peak_area" value="0"/>
20107 <param name="scoring_model" value="default"/>
20108 <param name="im_extra_drift" value="0.0"/>
20109 <section name="TransitionGroupPicker">
20110 <param name="stop_after_feature" value="-1"/>
20111 <param name="min_peak_width" value="-1.0"/>
20112 <param name="peak_integration" value="original"/>
20113 <param name="background_subtraction" value="none"/>
20114 <param name="recalculate_peaks" value="true"/>
20115 <param name="use_precursors" value="false"/>
20116 <param name="use_consensus" value="true"/>
20117 <param name="recalculate_peaks_max_z" value="0.75"/>
20118 <param name="minimal_quality" value="-1.5"/>
20119 <param name="resample_boundary" value="15.0"/>
20120 <param name="compute_peak_quality" value="true"/>
20121 <param name="compute_peak_shape_metrics" value="false"/>
20122 <param name="compute_total_mi" value="false"/>
20123 <param name="boundary_selection_method" value="largest"/>
20124 <section name="PeakPickerMRM">
20125 <param name="sgolay_frame_length" value="11"/>
20126 <param name="sgolay_polynomial_order" value="3"/>
20127 <param name="gauss_width" value="30.0"/>
20128 <param name="use_gauss" value="false"/>
20129 <param name="peak_width" value="-1.0"/>
20130 <param name="signal_to_noise" value="0.1"/>
20131 <param name="write_sn_log_messages" value="false"/>
20132 <param name="remove_overlapping_peaks" value="true"/>
20133 <param name="method" value="corrected"/>
20134 </section>
20135 <section name="PeakIntegrator">
20136 <param name="integration_type" value="intensity_sum"/>
20137 <param name="baseline_type" value="base_to_base"/>
20138 <param name="fit_EMG" value="false"/>
20139 </section>
20140 </section>
20141 <section name="DIAScoring">
20142 <param name="dia_extraction_window" value="0.05"/>
20143 <param name="dia_extraction_unit" value="Th"/>
20144 <param name="dia_centroided" value="false"/>
20145 <param name="dia_byseries_intensity_min" value="300.0"/>
20146 <param name="dia_byseries_ppm_diff" value="10.0"/>
20147 <param name="dia_nr_isotopes" value="4"/>
20148 <param name="dia_nr_charges" value="4"/>
20149 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20150 </section>
20151 <section name="EMGScoring">
20152 <param name="max_iteration" value="10"/>
20153 </section>
20154 <section name="Scores">
20155 <param name="use_shape_score" value="true"/>
20156 <param name="use_coelution_score" value="true"/>
20157 <param name="use_rt_score" value="true"/>
20158 <param name="use_library_score" value="true"/>
20159 <param name="use_intensity_score" value="true"/>
20160 <param name="use_nr_peaks_score" value="true"/>
20161 <param name="use_total_xic_score" value="true"/>
20162 <param name="use_total_mi_score" value="false"/>
20163 <param name="use_sn_score" value="true"/>
20164 <param name="use_mi_score" value="false"/>
20165 <param name="use_dia_scores" value="true"/>
20166 <param name="use_ms1_correlation" value="false"/>
20167 <param name="use_sonar_scores" value="false"/>
20168 <param name="use_ion_mobility_scores" value="false"/>
20169 <param name="use_ms1_fullscan" value="false"/>
20170 <param name="use_ms1_mi" value="false"/>
20171 <param name="use_uis_scores" value="false"/>
20172 </section>
20173 </section>
20174 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20175 <output name="ctd_out" ftype="xml">
20176 <assert_contents>
20177 <is_valid_xml/>
20178 </assert_contents>
20179 </output>
20180 </test>
20181 <test expect_num_outputs="3">
20182 <conditional name="adv_opts_cond">
20183 <param name="adv_opts_selector" value="advanced"/>
20184 <param name="sort_swath_maps" value="false"/>
20185 <param name="use_ms1_traces" value="false"/>
20186 <param name="enable_uis_scoring" value="false"/>
20187 <param name="out_chrom_type" value="mzML"/>
20188 <param name="min_upper_edge_dist" value="0.0"/>
20189 <param name="extra_rt_extraction_window" value="0.0"/>
20190 <param name="mz_extraction_window_unit" value="Th"/>
20191 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20192 <param name="use_ms1_ion_mobility" value="true"/>
20193 <param name="matching_window_only" value="false"/>
20194 <param name="irt_mz_extraction_window" value="550.0"/>
20195 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20196 <param name="irt_im_extraction_window" value="-1.0"/>
20197 <param name="min_rsq" value="0.95"/>
20198 <param name="min_coverage" value="0.6"/>
20199 <param name="split_file_input" value="false"/>
20200 <param name="use_elution_model_score" value="false"/>
20201 <param name="readOptions" value="normal"/>
20202 <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
20203 <param name="extraction_function" value="tophat"/>
20204 <param name="batchSize" value="250"/>
20205 <param name="ms1_isotopes" value="0"/>
20206 <param name="force" value="false"/>
20207 <param name="test" value="true"/>
20208 </conditional>
20209 <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
20210 <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
20211 <param name="tr_type" value=""/>
20212 <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
20213 <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20214 <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20215 <param name="sonar" value="true"/>
20216 <param name="rt_extraction_window" value="-1.0"/>
20217 <param name="ion_mobility_window" value="-1.0"/>
20218 <param name="mz_extraction_window" value="0.2"/>
20219 <param name="mz_extraction_window_ms1" value="0.05"/>
20220 <param name="im_extraction_window_ms1" value="-1.0"/>
20221 <section name="Debugging"/>
20222 <section name="Calibration">
20223 <param name="ms1_im_calibration" value="false"/>
20224 <param name="im_correction_function" value="linear"/>
20225 <param name="debug_im_file" value=""/>
20226 <param name="debug_mz_file" value=""/>
20227 </section>
20228 <section name="Library">
20229 <param name="retentionTimeInterpretation" value="iRT"/>
20230 <param name="override_group_label_check" value="false"/>
20231 <param name="force_invalid_mods" value="false"/>
20232 </section>
20233 <section name="RTNormalization">
20234 <param name="alignmentMethod" value="linear"/>
20235 <param name="outlierMethod" value="none"/>
20236 <param name="useIterativeChauvenet" value="false"/>
20237 <param name="RANSACMaxIterations" value="1000"/>
20238 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20239 <param name="RANSACSamplingSize" value="10"/>
20240 <param name="estimateBestPeptides" value="false"/>
20241 <param name="InitialQualityCutoff" value="0.5"/>
20242 <param name="OverallQualityCutoff" value="5.5"/>
20243 <param name="NrRTBins" value="10"/>
20244 <param name="MinPeptidesPerBin" value="1"/>
20245 <param name="MinBinsFilled" value="8"/>
20246 <section name="lowess">
20247 <param name="span" value="0.666666666666667"/>
20248 </section>
20249 <section name="b_spline">
20250 <param name="num_nodes" value="5"/>
20251 </section>
20252 </section>
20253 <section name="Scoring">
20254 <param name="stop_report_after_feature" value="5"/>
20255 <param name="rt_normalization_factor" value="100.0"/>
20256 <param name="quantification_cutoff" value="0.0"/>
20257 <param name="write_convex_hull" value="false"/>
20258 <param name="spectrum_addition_method" value="simple"/>
20259 <param name="add_up_spectra" value="1"/>
20260 <param name="spacing_for_spectra_resampling" value="0.005"/>
20261 <param name="uis_threshold_sn" value="0"/>
20262 <param name="uis_threshold_peak_area" value="0"/>
20263 <param name="scoring_model" value="default"/>
20264 <param name="im_extra_drift" value="0.0"/>
20265 <section name="TransitionGroupPicker">
20266 <param name="stop_after_feature" value="-1"/>
20267 <param name="min_peak_width" value="-1.0"/>
20268 <param name="peak_integration" value="original"/>
20269 <param name="background_subtraction" value="none"/>
20270 <param name="recalculate_peaks" value="true"/>
20271 <param name="use_precursors" value="false"/>
20272 <param name="use_consensus" value="true"/>
20273 <param name="recalculate_peaks_max_z" value="0.75"/>
20274 <param name="minimal_quality" value="-1.5"/>
20275 <param name="resample_boundary" value="15.0"/>
20276 <param name="compute_peak_quality" value="true"/>
20277 <param name="compute_peak_shape_metrics" value="false"/>
20278 <param name="compute_total_mi" value="false"/>
20279 <param name="boundary_selection_method" value="largest"/>
20280 <section name="PeakPickerMRM">
20281 <param name="sgolay_frame_length" value="11"/>
20282 <param name="sgolay_polynomial_order" value="3"/>
20283 <param name="gauss_width" value="30.0"/>
20284 <param name="use_gauss" value="false"/>
20285 <param name="peak_width" value="-1.0"/>
20286 <param name="signal_to_noise" value="0.1"/>
20287 <param name="write_sn_log_messages" value="false"/>
20288 <param name="remove_overlapping_peaks" value="true"/>
20289 <param name="method" value="corrected"/>
20290 </section>
20291 <section name="PeakIntegrator">
20292 <param name="integration_type" value="intensity_sum"/>
20293 <param name="baseline_type" value="base_to_base"/>
20294 <param name="fit_EMG" value="false"/>
20295 </section>
20296 </section>
20297 <section name="DIAScoring">
20298 <param name="dia_extraction_window" value="0.05"/>
20299 <param name="dia_extraction_unit" value="Th"/>
20300 <param name="dia_centroided" value="false"/>
20301 <param name="dia_byseries_intensity_min" value="300.0"/>
20302 <param name="dia_byseries_ppm_diff" value="10.0"/>
20303 <param name="dia_nr_isotopes" value="4"/>
20304 <param name="dia_nr_charges" value="4"/>
20305 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20306 </section>
20307 <section name="EMGScoring">
20308 <param name="max_iteration" value="10"/>
20309 </section>
20310 <section name="Scores">
20311 <param name="use_shape_score" value="true"/>
20312 <param name="use_coelution_score" value="true"/>
20313 <param name="use_rt_score" value="true"/>
20314 <param name="use_library_score" value="true"/>
20315 <param name="use_intensity_score" value="true"/>
20316 <param name="use_nr_peaks_score" value="true"/>
20317 <param name="use_total_xic_score" value="true"/>
20318 <param name="use_total_mi_score" value="false"/>
20319 <param name="use_sn_score" value="true"/>
20320 <param name="use_mi_score" value="false"/>
20321 <param name="use_dia_scores" value="true"/>
20322 <param name="use_ms1_correlation" value="false"/>
20323 <param name="use_sonar_scores" value="true"/>
20324 <param name="use_ion_mobility_scores" value="false"/>
20325 <param name="use_ms1_fullscan" value="false"/>
20326 <param name="use_ms1_mi" value="false"/>
20327 <param name="use_uis_scores" value="false"/>
20328 </section>
20329 </section>
20330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20331 <output name="ctd_out" ftype="xml">
20332 <assert_contents>
20333 <is_valid_xml/>
20334 </assert_contents>
20335 </output>
20336 </test>
20337 <test expect_num_outputs="3">
20338 <conditional name="adv_opts_cond">
20339 <param name="adv_opts_selector" value="advanced"/>
20340 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20341 <param name="sort_swath_maps" value="false"/>
20342 <param name="use_ms1_traces" value="true"/>
20343 <param name="enable_uis_scoring" value="false"/>
20344 <param name="out_chrom_type" value="mzML"/>
20345 <param name="min_upper_edge_dist" value="0.0"/>
20346 <param name="extra_rt_extraction_window" value="0.0"/>
20347 <param name="mz_extraction_window_unit" value="Th"/>
20348 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20349 <param name="use_ms1_ion_mobility" value="true"/>
20350 <param name="matching_window_only" value="false"/>
20351 <param name="irt_mz_extraction_window" value="0.05"/>
20352 <param name="irt_mz_extraction_window_unit" value="Th"/>
20353 <param name="irt_im_extraction_window" value="-1.0"/>
20354 <param name="min_rsq" value="0.95"/>
20355 <param name="min_coverage" value="0.6"/>
20356 <param name="split_file_input" value="false"/>
20357 <param name="use_elution_model_score" value="false"/>
20358 <param name="readOptions" value="normal"/>
20359 <param name="mz_correction_function" value="none"/>
20360 <param name="extraction_function" value="tophat"/>
20361 <param name="batchSize" value="250"/>
20362 <param name="ms1_isotopes" value="0"/>
20363 <param name="force" value="false"/>
20364 <param name="test" value="true"/>
20365 </conditional>
20366 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20367 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
20368 <param name="tr_type" value="pqp"/>
20369 <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
20370 <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20371 <param name="sonar" value="false"/>
20372 <param name="rt_extraction_window" value="600.0"/>
20373 <param name="ion_mobility_window" value="-1.0"/>
20374 <param name="mz_extraction_window" value="0.05"/>
20375 <param name="mz_extraction_window_ms1" value="0.05"/>
20376 <param name="im_extraction_window_ms1" value="-1.0"/>
20377 <section name="Debugging"/>
20378 <section name="Calibration">
20379 <param name="ms1_im_calibration" value="false"/>
20380 <param name="im_correction_function" value="linear"/>
20381 <param name="debug_im_file" value=""/>
20382 <param name="debug_mz_file" value=""/>
20383 </section>
20384 <section name="Library">
20385 <param name="retentionTimeInterpretation" value="iRT"/>
20386 <param name="override_group_label_check" value="false"/>
20387 <param name="force_invalid_mods" value="false"/>
20388 </section>
20389 <section name="RTNormalization">
20390 <param name="alignmentMethod" value="linear"/>
20391 <param name="outlierMethod" value="iter_residual"/>
20392 <param name="useIterativeChauvenet" value="false"/>
20393 <param name="RANSACMaxIterations" value="1000"/>
20394 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20395 <param name="RANSACSamplingSize" value="10"/>
20396 <param name="estimateBestPeptides" value="false"/>
20397 <param name="InitialQualityCutoff" value="0.5"/>
20398 <param name="OverallQualityCutoff" value="5.5"/>
20399 <param name="NrRTBins" value="10"/>
20400 <param name="MinPeptidesPerBin" value="1"/>
20401 <param name="MinBinsFilled" value="8"/>
20402 <section name="lowess">
20403 <param name="span" value="0.666666666666667"/>
20404 </section>
20405 <section name="b_spline">
20406 <param name="num_nodes" value="5"/>
20407 </section>
20408 </section>
20409 <section name="Scoring">
20410 <param name="stop_report_after_feature" value="5"/>
20411 <param name="rt_normalization_factor" value="100.0"/>
20412 <param name="quantification_cutoff" value="0.0"/>
20413 <param name="write_convex_hull" value="false"/>
20414 <param name="spectrum_addition_method" value="simple"/>
20415 <param name="add_up_spectra" value="1"/>
20416 <param name="spacing_for_spectra_resampling" value="0.005"/>
20417 <param name="uis_threshold_sn" value="0"/>
20418 <param name="uis_threshold_peak_area" value="0"/>
20419 <param name="scoring_model" value="default"/>
20420 <param name="im_extra_drift" value="0.0"/>
20421 <section name="TransitionGroupPicker">
20422 <param name="stop_after_feature" value="-1"/>
20423 <param name="min_peak_width" value="-1.0"/>
20424 <param name="peak_integration" value="original"/>
20425 <param name="background_subtraction" value="none"/>
20426 <param name="recalculate_peaks" value="true"/>
20427 <param name="use_precursors" value="false"/>
20428 <param name="use_consensus" value="true"/>
20429 <param name="recalculate_peaks_max_z" value="0.75"/>
20430 <param name="minimal_quality" value="-1.5"/>
20431 <param name="resample_boundary" value="15.0"/>
20432 <param name="compute_peak_quality" value="true"/>
20433 <param name="compute_peak_shape_metrics" value="false"/>
20434 <param name="compute_total_mi" value="false"/>
20435 <param name="boundary_selection_method" value="largest"/>
20436 <section name="PeakPickerMRM">
20437 <param name="sgolay_frame_length" value="11"/>
20438 <param name="sgolay_polynomial_order" value="3"/>
20439 <param name="gauss_width" value="30.0"/>
20440 <param name="use_gauss" value="false"/>
20441 <param name="peak_width" value="-1.0"/>
20442 <param name="signal_to_noise" value="0.1"/>
20443 <param name="write_sn_log_messages" value="false"/>
20444 <param name="remove_overlapping_peaks" value="true"/>
20445 <param name="method" value="corrected"/>
20446 </section>
20447 <section name="PeakIntegrator">
20448 <param name="integration_type" value="intensity_sum"/>
20449 <param name="baseline_type" value="base_to_base"/>
20450 <param name="fit_EMG" value="false"/>
20451 </section>
20452 </section>
20453 <section name="DIAScoring">
20454 <param name="dia_extraction_window" value="0.05"/>
20455 <param name="dia_extraction_unit" value="Th"/>
20456 <param name="dia_centroided" value="false"/>
20457 <param name="dia_byseries_intensity_min" value="300.0"/>
20458 <param name="dia_byseries_ppm_diff" value="10.0"/>
20459 <param name="dia_nr_isotopes" value="4"/>
20460 <param name="dia_nr_charges" value="4"/>
20461 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20462 </section>
20463 <section name="EMGScoring">
20464 <param name="max_iteration" value="10"/>
20465 </section>
20466 <section name="Scores">
20467 <param name="use_shape_score" value="true"/>
20468 <param name="use_coelution_score" value="true"/>
20469 <param name="use_rt_score" value="true"/>
20470 <param name="use_library_score" value="true"/>
20471 <param name="use_intensity_score" value="true"/>
20472 <param name="use_nr_peaks_score" value="true"/>
20473 <param name="use_total_xic_score" value="true"/>
20474 <param name="use_total_mi_score" value="false"/>
20475 <param name="use_sn_score" value="true"/>
20476 <param name="use_mi_score" value="false"/>
20477 <param name="use_dia_scores" value="true"/>
20478 <param name="use_ms1_correlation" value="false"/>
20479 <param name="use_sonar_scores" value="false"/>
20480 <param name="use_ion_mobility_scores" value="false"/>
20481 <param name="use_ms1_fullscan" value="false"/>
20482 <param name="use_ms1_mi" value="false"/>
20483 <param name="use_uis_scores" value="false"/>
20484 </section>
20485 </section>
20486 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
20487 <output name="ctd_out" ftype="xml">
20488 <assert_contents>
20489 <is_valid_xml/>
20490 </assert_contents>
20491 </output>
20492 </test>
20493 <test expect_num_outputs="3">
20494 <conditional name="adv_opts_cond">
20495 <param name="adv_opts_selector" value="advanced"/>
20496 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20497 <param name="sort_swath_maps" value="false"/>
20498 <param name="use_ms1_traces" value="true"/>
20499 <param name="enable_uis_scoring" value="false"/>
20500 <param name="out_chrom_type" value="sqMass"/>
20501 <param name="min_upper_edge_dist" value="0.0"/>
20502 <param name="extra_rt_extraction_window" value="0.0"/>
20503 <param name="mz_extraction_window_unit" value="Th"/>
20504 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20505 <param name="use_ms1_ion_mobility" value="true"/>
20506 <param name="matching_window_only" value="false"/>
20507 <param name="irt_mz_extraction_window" value="0.05"/>
20508 <param name="irt_mz_extraction_window_unit" value="Th"/>
20509 <param name="irt_im_extraction_window" value="-1.0"/>
20510 <param name="min_rsq" value="0.95"/>
20511 <param name="min_coverage" value="0.6"/>
20512 <param name="split_file_input" value="false"/>
20513 <param name="use_elution_model_score" value="false"/>
20514 <param name="readOptions" value="normal"/>
20515 <param name="mz_correction_function" value="none"/>
20516 <param name="extraction_function" value="tophat"/>
20517 <param name="batchSize" value="250"/>
20518 <param name="ms1_isotopes" value="0"/>
20519 <param name="force" value="false"/>
20520 <param name="test" value="true"/>
20521 </conditional>
20522 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20523 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
20524 <param name="tr_type" value="pqp"/>
20525 <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
20526 <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
20527 <param name="sonar" value="false"/>
20528 <param name="rt_extraction_window" value="600.0"/>
20529 <param name="ion_mobility_window" value="-1.0"/>
20530 <param name="mz_extraction_window" value="0.05"/>
20531 <param name="mz_extraction_window_ms1" value="0.05"/>
20532 <param name="im_extraction_window_ms1" value="-1.0"/>
20533 <section name="Debugging"/>
20534 <section name="Calibration">
20535 <param name="ms1_im_calibration" value="false"/>
20536 <param name="im_correction_function" value="linear"/>
20537 <param name="debug_im_file" value=""/>
20538 <param name="debug_mz_file" value=""/>
20539 </section>
20540 <section name="Library">
20541 <param name="retentionTimeInterpretation" value="iRT"/>
20542 <param name="override_group_label_check" value="false"/>
20543 <param name="force_invalid_mods" value="false"/>
20544 </section>
20545 <section name="RTNormalization">
20546 <param name="alignmentMethod" value="linear"/>
20547 <param name="outlierMethod" value="iter_residual"/>
20548 <param name="useIterativeChauvenet" value="false"/>
20549 <param name="RANSACMaxIterations" value="1000"/>
20550 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20551 <param name="RANSACSamplingSize" value="10"/>
20552 <param name="estimateBestPeptides" value="false"/>
20553 <param name="InitialQualityCutoff" value="0.5"/>
20554 <param name="OverallQualityCutoff" value="5.5"/>
20555 <param name="NrRTBins" value="10"/>
20556 <param name="MinPeptidesPerBin" value="1"/>
20557 <param name="MinBinsFilled" value="8"/>
20558 <section name="lowess">
20559 <param name="span" value="0.666666666666667"/>
20560 </section>
20561 <section name="b_spline">
20562 <param name="num_nodes" value="5"/>
20563 </section>
20564 </section>
20565 <section name="Scoring">
20566 <param name="stop_report_after_feature" value="5"/>
20567 <param name="rt_normalization_factor" value="100.0"/>
20568 <param name="quantification_cutoff" value="0.0"/>
20569 <param name="write_convex_hull" value="false"/>
20570 <param name="spectrum_addition_method" value="simple"/>
20571 <param name="add_up_spectra" value="1"/>
20572 <param name="spacing_for_spectra_resampling" value="0.005"/>
20573 <param name="uis_threshold_sn" value="0"/>
20574 <param name="uis_threshold_peak_area" value="0"/>
20575 <param name="scoring_model" value="default"/>
20576 <param name="im_extra_drift" value="0.0"/>
20577 <section name="TransitionGroupPicker">
20578 <param name="stop_after_feature" value="-1"/>
20579 <param name="min_peak_width" value="-1.0"/>
20580 <param name="peak_integration" value="original"/>
20581 <param name="background_subtraction" value="none"/>
20582 <param name="recalculate_peaks" value="true"/>
20583 <param name="use_precursors" value="false"/>
20584 <param name="use_consensus" value="true"/>
20585 <param name="recalculate_peaks_max_z" value="0.75"/>
20586 <param name="minimal_quality" value="-1.5"/>
20587 <param name="resample_boundary" value="15.0"/>
20588 <param name="compute_peak_quality" value="true"/>
20589 <param name="compute_peak_shape_metrics" value="false"/>
20590 <param name="compute_total_mi" value="false"/>
20591 <param name="boundary_selection_method" value="largest"/>
20592 <section name="PeakPickerMRM">
20593 <param name="sgolay_frame_length" value="11"/>
20594 <param name="sgolay_polynomial_order" value="3"/>
20595 <param name="gauss_width" value="30.0"/>
20596 <param name="use_gauss" value="false"/>
20597 <param name="peak_width" value="-1.0"/>
20598 <param name="signal_to_noise" value="0.1"/>
20599 <param name="write_sn_log_messages" value="false"/>
20600 <param name="remove_overlapping_peaks" value="true"/>
20601 <param name="method" value="corrected"/>
20602 </section>
20603 <section name="PeakIntegrator">
20604 <param name="integration_type" value="intensity_sum"/>
20605 <param name="baseline_type" value="base_to_base"/>
20606 <param name="fit_EMG" value="false"/>
20607 </section>
20608 </section>
20609 <section name="DIAScoring">
20610 <param name="dia_extraction_window" value="0.05"/>
20611 <param name="dia_extraction_unit" value="Th"/>
20612 <param name="dia_centroided" value="false"/>
20613 <param name="dia_byseries_intensity_min" value="300.0"/>
20614 <param name="dia_byseries_ppm_diff" value="10.0"/>
20615 <param name="dia_nr_isotopes" value="4"/>
20616 <param name="dia_nr_charges" value="4"/>
20617 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20618 </section>
20619 <section name="EMGScoring">
20620 <param name="max_iteration" value="10"/>
20621 </section>
20622 <section name="Scores">
20623 <param name="use_shape_score" value="true"/>
20624 <param name="use_coelution_score" value="true"/>
20625 <param name="use_rt_score" value="true"/>
20626 <param name="use_library_score" value="true"/>
20627 <param name="use_intensity_score" value="true"/>
20628 <param name="use_nr_peaks_score" value="true"/>
20629 <param name="use_total_xic_score" value="true"/>
20630 <param name="use_total_mi_score" value="false"/>
20631 <param name="use_sn_score" value="true"/>
20632 <param name="use_mi_score" value="false"/>
20633 <param name="use_dia_scores" value="true"/>
20634 <param name="use_ms1_correlation" value="false"/>
20635 <param name="use_sonar_scores" value="false"/>
20636 <param name="use_ion_mobility_scores" value="false"/>
20637 <param name="use_ms1_fullscan" value="false"/>
20638 <param name="use_ms1_mi" value="false"/>
20639 <param name="use_uis_scores" value="false"/>
20640 </section>
20641 </section>
20642 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
20643 <output name="ctd_out" ftype="xml">
20644 <assert_contents>
20645 <is_valid_xml/>
20646 </assert_contents>
20647 </output>
20648 </test>
20649 <test expect_num_outputs="3">
20650 <conditional name="adv_opts_cond">
20651 <param name="adv_opts_selector" value="advanced"/>
20652 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20653 <param name="sort_swath_maps" value="false"/>
20654 <param name="use_ms1_traces" value="true"/>
20655 <param name="enable_uis_scoring" value="false"/>
20656 <param name="out_chrom_type" value="mzML"/>
20657 <param name="min_upper_edge_dist" value="0.0"/>
20658 <param name="extra_rt_extraction_window" value="0.0"/>
20659 <param name="mz_extraction_window_unit" value="Th"/>
20660 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20661 <param name="use_ms1_ion_mobility" value="true"/>
20662 <param name="matching_window_only" value="false"/>
20663 <param name="irt_mz_extraction_window" value="0.05"/>
20664 <param name="irt_mz_extraction_window_unit" value="Th"/>
20665 <param name="irt_im_extraction_window" value="-1.0"/>
20666 <param name="min_rsq" value="0.95"/>
20667 <param name="min_coverage" value="0.6"/>
20668 <param name="split_file_input" value="false"/>
20669 <param name="use_elution_model_score" value="false"/>
20670 <param name="readOptions" value="normal"/>
20671 <param name="mz_correction_function" value="none"/>
20672 <param name="extraction_function" value="tophat"/>
20673 <param name="batchSize" value="250"/>
20674 <param name="ms1_isotopes" value="2"/>
20675 <param name="force" value="false"/>
20676 <param name="test" value="true"/>
20677 </conditional>
20678 <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
20679 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20680 <param name="tr_type" value=""/>
20681 <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20682 <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20683 <param name="sonar" value="false"/>
20684 <param name="rt_extraction_window" value="600.0"/>
20685 <param name="ion_mobility_window" value="-1.0"/>
20686 <param name="mz_extraction_window" value="0.05"/>
20687 <param name="mz_extraction_window_ms1" value="0.05"/>
20688 <param name="im_extraction_window_ms1" value="-1.0"/>
20689 <section name="Debugging"/>
20690 <section name="Calibration">
20691 <param name="ms1_im_calibration" value="false"/>
20692 <param name="im_correction_function" value="linear"/>
20693 <param name="debug_im_file" value=""/>
20694 <param name="debug_mz_file" value=""/>
20695 </section>
20696 <section name="Library">
20697 <param name="retentionTimeInterpretation" value="iRT"/>
20698 <param name="override_group_label_check" value="false"/>
20699 <param name="force_invalid_mods" value="false"/>
20700 </section>
20701 <section name="RTNormalization">
20702 <param name="alignmentMethod" value="linear"/>
20703 <param name="outlierMethod" value="iter_residual"/>
20704 <param name="useIterativeChauvenet" value="false"/>
20705 <param name="RANSACMaxIterations" value="1000"/>
20706 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20707 <param name="RANSACSamplingSize" value="10"/>
20708 <param name="estimateBestPeptides" value="false"/>
20709 <param name="InitialQualityCutoff" value="0.5"/>
20710 <param name="OverallQualityCutoff" value="5.5"/>
20711 <param name="NrRTBins" value="10"/>
20712 <param name="MinPeptidesPerBin" value="1"/>
20713 <param name="MinBinsFilled" value="8"/>
20714 <section name="lowess">
20715 <param name="span" value="0.666666666666667"/>
20716 </section>
20717 <section name="b_spline">
20718 <param name="num_nodes" value="5"/>
20719 </section>
20720 </section>
20721 <section name="Scoring">
20722 <param name="stop_report_after_feature" value="5"/>
20723 <param name="rt_normalization_factor" value="100.0"/>
20724 <param name="quantification_cutoff" value="0.0"/>
20725 <param name="write_convex_hull" value="false"/>
20726 <param name="spectrum_addition_method" value="simple"/>
20727 <param name="add_up_spectra" value="1"/>
20728 <param name="spacing_for_spectra_resampling" value="0.005"/>
20729 <param name="uis_threshold_sn" value="0"/>
20730 <param name="uis_threshold_peak_area" value="0"/>
20731 <param name="scoring_model" value="default"/>
20732 <param name="im_extra_drift" value="0.0"/>
20733 <section name="TransitionGroupPicker">
20734 <param name="stop_after_feature" value="-1"/>
20735 <param name="min_peak_width" value="-1.0"/>
20736 <param name="peak_integration" value="original"/>
20737 <param name="background_subtraction" value="none"/>
20738 <param name="recalculate_peaks" value="true"/>
20739 <param name="use_precursors" value="true"/>
20740 <param name="use_consensus" value="true"/> 22977 <param name="use_consensus" value="true"/>
20741 <param name="recalculate_peaks_max_z" value="0.75"/> 22978 <param name="recalculate_peaks_max_z" value="0.75"/>
20742 <param name="minimal_quality" value="-1.5"/> 22979 <param name="minimal_quality" value="-1.5"/>
20743 <param name="resample_boundary" value="15.0"/> 22980 <param name="resample_boundary" value="15.0"/>
20744 <param name="compute_peak_quality" value="false"/> 22981 <param name="compute_peak_quality" value="false"/>
20783 <param name="use_intensity_score" value="true"/> 23020 <param name="use_intensity_score" value="true"/>
20784 <param name="use_nr_peaks_score" value="true"/> 23021 <param name="use_nr_peaks_score" value="true"/>
20785 <param name="use_total_xic_score" value="true"/> 23022 <param name="use_total_xic_score" value="true"/>
20786 <param name="use_total_mi_score" value="false"/> 23023 <param name="use_total_mi_score" value="false"/>
20787 <param name="use_sn_score" value="true"/> 23024 <param name="use_sn_score" value="true"/>
20788 <param name="use_mi_score" value="false"/> 23025 <param name="use_mi_score" value="true"/>
20789 <param name="use_dia_scores" value="true"/>
20790 <param name="use_ms1_correlation" value="false"/>
20791 <param name="use_sonar_scores" value="false"/>
20792 <param name="use_ion_mobility_scores" value="false"/>
20793 <param name="use_ms1_fullscan" value="false"/>
20794 <param name="use_ms1_mi" value="false"/>
20795 <param name="use_uis_scores" value="false"/>
20796 </section>
20797 </section>
20798 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20799 <output name="ctd_out" ftype="xml">
20800 <assert_contents>
20801 <is_valid_xml/>
20802 </assert_contents>
20803 </output>
20804 </test>
20805 <test expect_num_outputs="3">
20806 <conditional name="adv_opts_cond">
20807 <param name="adv_opts_selector" value="advanced"/>
20808 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20809 <param name="sort_swath_maps" value="false"/>
20810 <param name="use_ms1_traces" value="true"/>
20811 <param name="enable_uis_scoring" value="false"/>
20812 <param name="out_chrom_type" value="mzML"/>
20813 <param name="min_upper_edge_dist" value="0.0"/>
20814 <param name="extra_rt_extraction_window" value="0.0"/>
20815 <param name="mz_extraction_window_unit" value="Th"/>
20816 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20817 <param name="use_ms1_ion_mobility" value="true"/>
20818 <param name="matching_window_only" value="false"/>
20819 <param name="irt_mz_extraction_window" value="0.05"/>
20820 <param name="irt_mz_extraction_window_unit" value="Th"/>
20821 <param name="irt_im_extraction_window" value="-1.0"/>
20822 <param name="min_rsq" value="0.95"/>
20823 <param name="min_coverage" value="0.6"/>
20824 <param name="split_file_input" value="false"/>
20825 <param name="use_elution_model_score" value="false"/>
20826 <param name="readOptions" value="workingInMemory"/>
20827 <param name="mz_correction_function" value="none"/>
20828 <param name="extraction_function" value="tophat"/>
20829 <param name="batchSize" value="250"/>
20830 <param name="ms1_isotopes" value="2"/>
20831 <param name="force" value="false"/>
20832 <param name="test" value="true"/>
20833 </conditional>
20834 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
20835 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20836 <param name="tr_type" value=""/>
20837 <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20838 <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20839 <param name="sonar" value="false"/>
20840 <param name="rt_extraction_window" value="600.0"/>
20841 <param name="ion_mobility_window" value="-1.0"/>
20842 <param name="mz_extraction_window" value="0.05"/>
20843 <param name="mz_extraction_window_ms1" value="0.05"/>
20844 <param name="im_extraction_window_ms1" value="-1.0"/>
20845 <section name="Debugging"/>
20846 <section name="Calibration">
20847 <param name="ms1_im_calibration" value="false"/>
20848 <param name="im_correction_function" value="linear"/>
20849 <param name="debug_im_file" value=""/>
20850 <param name="debug_mz_file" value=""/>
20851 </section>
20852 <section name="Library">
20853 <param name="retentionTimeInterpretation" value="iRT"/>
20854 <param name="override_group_label_check" value="false"/>
20855 <param name="force_invalid_mods" value="false"/>
20856 </section>
20857 <section name="RTNormalization">
20858 <param name="alignmentMethod" value="linear"/>
20859 <param name="outlierMethod" value="iter_residual"/>
20860 <param name="useIterativeChauvenet" value="false"/>
20861 <param name="RANSACMaxIterations" value="1000"/>
20862 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20863 <param name="RANSACSamplingSize" value="10"/>
20864 <param name="estimateBestPeptides" value="false"/>
20865 <param name="InitialQualityCutoff" value="0.5"/>
20866 <param name="OverallQualityCutoff" value="5.5"/>
20867 <param name="NrRTBins" value="10"/>
20868 <param name="MinPeptidesPerBin" value="1"/>
20869 <param name="MinBinsFilled" value="8"/>
20870 <section name="lowess">
20871 <param name="span" value="0.666666666666667"/>
20872 </section>
20873 <section name="b_spline">
20874 <param name="num_nodes" value="5"/>
20875 </section>
20876 </section>
20877 <section name="Scoring">
20878 <param name="stop_report_after_feature" value="5"/>
20879 <param name="rt_normalization_factor" value="100.0"/>
20880 <param name="quantification_cutoff" value="0.0"/>
20881 <param name="write_convex_hull" value="false"/>
20882 <param name="spectrum_addition_method" value="simple"/>
20883 <param name="add_up_spectra" value="1"/>
20884 <param name="spacing_for_spectra_resampling" value="0.005"/>
20885 <param name="uis_threshold_sn" value="0"/>
20886 <param name="uis_threshold_peak_area" value="0"/>
20887 <param name="scoring_model" value="default"/>
20888 <param name="im_extra_drift" value="0.0"/>
20889 <section name="TransitionGroupPicker">
20890 <param name="stop_after_feature" value="-1"/>
20891 <param name="min_peak_width" value="-1.0"/>
20892 <param name="peak_integration" value="original"/>
20893 <param name="background_subtraction" value="none"/>
20894 <param name="recalculate_peaks" value="true"/>
20895 <param name="use_precursors" value="false"/>
20896 <param name="use_consensus" value="true"/>
20897 <param name="recalculate_peaks_max_z" value="0.75"/>
20898 <param name="minimal_quality" value="-1.5"/>
20899 <param name="resample_boundary" value="15.0"/>
20900 <param name="compute_peak_quality" value="true"/>
20901 <param name="compute_peak_shape_metrics" value="false"/>
20902 <param name="compute_total_mi" value="false"/>
20903 <param name="boundary_selection_method" value="largest"/>
20904 <section name="PeakPickerMRM">
20905 <param name="sgolay_frame_length" value="11"/>
20906 <param name="sgolay_polynomial_order" value="3"/>
20907 <param name="gauss_width" value="30.0"/>
20908 <param name="use_gauss" value="false"/>
20909 <param name="peak_width" value="-1.0"/>
20910 <param name="signal_to_noise" value="0.1"/>
20911 <param name="write_sn_log_messages" value="false"/>
20912 <param name="remove_overlapping_peaks" value="true"/>
20913 <param name="method" value="corrected"/>
20914 </section>
20915 <section name="PeakIntegrator">
20916 <param name="integration_type" value="intensity_sum"/>
20917 <param name="baseline_type" value="base_to_base"/>
20918 <param name="fit_EMG" value="false"/>
20919 </section>
20920 </section>
20921 <section name="DIAScoring">
20922 <param name="dia_extraction_window" value="0.05"/>
20923 <param name="dia_extraction_unit" value="Th"/>
20924 <param name="dia_centroided" value="false"/>
20925 <param name="dia_byseries_intensity_min" value="300.0"/>
20926 <param name="dia_byseries_ppm_diff" value="10.0"/>
20927 <param name="dia_nr_isotopes" value="4"/>
20928 <param name="dia_nr_charges" value="4"/>
20929 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20930 </section>
20931 <section name="EMGScoring">
20932 <param name="max_iteration" value="10"/>
20933 </section>
20934 <section name="Scores">
20935 <param name="use_shape_score" value="true"/>
20936 <param name="use_coelution_score" value="true"/>
20937 <param name="use_rt_score" value="true"/>
20938 <param name="use_library_score" value="true"/>
20939 <param name="use_intensity_score" value="true"/>
20940 <param name="use_nr_peaks_score" value="true"/>
20941 <param name="use_total_xic_score" value="true"/>
20942 <param name="use_total_mi_score" value="false"/>
20943 <param name="use_sn_score" value="true"/>
20944 <param name="use_mi_score" value="false"/>
20945 <param name="use_dia_scores" value="true"/>
20946 <param name="use_ms1_correlation" value="false"/>
20947 <param name="use_sonar_scores" value="false"/>
20948 <param name="use_ion_mobility_scores" value="false"/>
20949 <param name="use_ms1_fullscan" value="false"/>
20950 <param name="use_ms1_mi" value="false"/>
20951 <param name="use_uis_scores" value="false"/>
20952 </section>
20953 </section>
20954 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20955 <output name="ctd_out" ftype="xml">
20956 <assert_contents>
20957 <is_valid_xml/>
20958 </assert_contents>
20959 </output>
20960 </test>
20961 <test expect_num_outputs="3">
20962 <conditional name="adv_opts_cond">
20963 <param name="adv_opts_selector" value="advanced"/>
20964 <param name="sort_swath_maps" value="false"/>
20965 <param name="use_ms1_traces" value="true"/>
20966 <param name="enable_uis_scoring" value="false"/>
20967 <param name="out_chrom_type" value="mzML"/>
20968 <param name="min_upper_edge_dist" value="0.0"/>
20969 <param name="extra_rt_extraction_window" value="0.0"/>
20970 <param name="mz_extraction_window_unit" value="Th"/>
20971 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20972 <param name="use_ms1_ion_mobility" value="false"/>
20973 <param name="matching_window_only" value="false"/>
20974 <param name="irt_mz_extraction_window" value="0.05"/>
20975 <param name="irt_mz_extraction_window_unit" value="Th"/>
20976 <param name="irt_im_extraction_window" value="-1.0"/>
20977 <param name="min_rsq" value="0.95"/>
20978 <param name="min_coverage" value="0.6"/>
20979 <param name="split_file_input" value="false"/>
20980 <param name="use_elution_model_score" value="false"/>
20981 <param name="readOptions" value="workingInMemory"/>
20982 <param name="mz_correction_function" value="none"/>
20983 <param name="extraction_function" value="tophat"/>
20984 <param name="batchSize" value="250"/>
20985 <param name="ms1_isotopes" value="0"/>
20986 <param name="force" value="false"/>
20987 <param name="test" value="true"/>
20988 </conditional>
20989 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
20990 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
20991 <param name="tr_type" value=""/>
20992 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20993 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20994 <param name="sonar" value="false"/>
20995 <param name="rt_extraction_window" value="600.0"/>
20996 <param name="ion_mobility_window" value="0.05"/>
20997 <param name="mz_extraction_window" value="0.05"/>
20998 <param name="mz_extraction_window_ms1" value="0.05"/>
20999 <param name="im_extraction_window_ms1" value="-1.0"/>
21000 <section name="Debugging"/>
21001 <section name="Calibration">
21002 <param name="ms1_im_calibration" value="false"/>
21003 <param name="im_correction_function" value="linear"/>
21004 <param name="debug_im_file" value=""/>
21005 <param name="debug_mz_file" value=""/>
21006 </section>
21007 <section name="Library">
21008 <param name="retentionTimeInterpretation" value="iRT"/>
21009 <param name="override_group_label_check" value="false"/>
21010 <param name="force_invalid_mods" value="false"/>
21011 </section>
21012 <section name="RTNormalization">
21013 <param name="alignmentMethod" value="linear"/>
21014 <param name="outlierMethod" value="iter_residual"/>
21015 <param name="useIterativeChauvenet" value="false"/>
21016 <param name="RANSACMaxIterations" value="1000"/>
21017 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21018 <param name="RANSACSamplingSize" value="10"/>
21019 <param name="estimateBestPeptides" value="false"/>
21020 <param name="InitialQualityCutoff" value="0.5"/>
21021 <param name="OverallQualityCutoff" value="5.5"/>
21022 <param name="NrRTBins" value="10"/>
21023 <param name="MinPeptidesPerBin" value="1"/>
21024 <param name="MinBinsFilled" value="8"/>
21025 <section name="lowess">
21026 <param name="span" value="0.666666666666667"/>
21027 </section>
21028 <section name="b_spline">
21029 <param name="num_nodes" value="5"/>
21030 </section>
21031 </section>
21032 <section name="Scoring">
21033 <param name="stop_report_after_feature" value="5"/>
21034 <param name="rt_normalization_factor" value="100.0"/>
21035 <param name="quantification_cutoff" value="0.0"/>
21036 <param name="write_convex_hull" value="false"/>
21037 <param name="spectrum_addition_method" value="simple"/>
21038 <param name="add_up_spectra" value="1"/>
21039 <param name="spacing_for_spectra_resampling" value="0.005"/>
21040 <param name="uis_threshold_sn" value="0"/>
21041 <param name="uis_threshold_peak_area" value="0"/>
21042 <param name="scoring_model" value="default"/>
21043 <param name="im_extra_drift" value="0.0"/>
21044 <section name="TransitionGroupPicker">
21045 <param name="stop_after_feature" value="-1"/>
21046 <param name="min_peak_width" value="-1.0"/>
21047 <param name="peak_integration" value="original"/>
21048 <param name="background_subtraction" value="none"/>
21049 <param name="recalculate_peaks" value="true"/>
21050 <param name="use_precursors" value="false"/>
21051 <param name="use_consensus" value="true"/>
21052 <param name="recalculate_peaks_max_z" value="0.75"/>
21053 <param name="minimal_quality" value="-1.5"/>
21054 <param name="resample_boundary" value="15.0"/>
21055 <param name="compute_peak_quality" value="true"/>
21056 <param name="compute_peak_shape_metrics" value="false"/>
21057 <param name="compute_total_mi" value="false"/>
21058 <param name="boundary_selection_method" value="largest"/>
21059 <section name="PeakPickerMRM">
21060 <param name="sgolay_frame_length" value="11"/>
21061 <param name="sgolay_polynomial_order" value="3"/>
21062 <param name="gauss_width" value="30.0"/>
21063 <param name="use_gauss" value="false"/>
21064 <param name="peak_width" value="-1.0"/>
21065 <param name="signal_to_noise" value="0.1"/>
21066 <param name="write_sn_log_messages" value="false"/>
21067 <param name="remove_overlapping_peaks" value="true"/>
21068 <param name="method" value="corrected"/>
21069 </section>
21070 <section name="PeakIntegrator">
21071 <param name="integration_type" value="intensity_sum"/>
21072 <param name="baseline_type" value="base_to_base"/>
21073 <param name="fit_EMG" value="false"/>
21074 </section>
21075 </section>
21076 <section name="DIAScoring">
21077 <param name="dia_extraction_window" value="0.05"/>
21078 <param name="dia_extraction_unit" value="Th"/>
21079 <param name="dia_centroided" value="false"/>
21080 <param name="dia_byseries_intensity_min" value="300.0"/>
21081 <param name="dia_byseries_ppm_diff" value="10.0"/>
21082 <param name="dia_nr_isotopes" value="4"/>
21083 <param name="dia_nr_charges" value="4"/>
21084 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21085 </section>
21086 <section name="EMGScoring">
21087 <param name="max_iteration" value="10"/>
21088 </section>
21089 <section name="Scores">
21090 <param name="use_shape_score" value="true"/>
21091 <param name="use_coelution_score" value="true"/>
21092 <param name="use_rt_score" value="true"/>
21093 <param name="use_library_score" value="true"/>
21094 <param name="use_intensity_score" value="true"/>
21095 <param name="use_nr_peaks_score" value="true"/>
21096 <param name="use_total_xic_score" value="true"/>
21097 <param name="use_total_mi_score" value="false"/>
21098 <param name="use_sn_score" value="true"/>
21099 <param name="use_mi_score" value="false"/>
21100 <param name="use_dia_scores" value="true"/>
21101 <param name="use_ms1_correlation" value="false"/>
21102 <param name="use_sonar_scores" value="false"/>
21103 <param name="use_ion_mobility_scores" value="true"/>
21104 <param name="use_ms1_fullscan" value="false"/>
21105 <param name="use_ms1_mi" value="false"/>
21106 <param name="use_uis_scores" value="false"/>
21107 </section>
21108 </section>
21109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21110 <output name="ctd_out" ftype="xml">
21111 <assert_contents>
21112 <is_valid_xml/>
21113 </assert_contents>
21114 </output>
21115 </test>
21116 <test expect_num_outputs="3">
21117 <conditional name="adv_opts_cond">
21118 <param name="adv_opts_selector" value="advanced"/>
21119 <param name="sort_swath_maps" value="false"/>
21120 <param name="use_ms1_traces" value="true"/>
21121 <param name="enable_uis_scoring" value="false"/>
21122 <param name="out_chrom_type" value="mzML"/>
21123 <param name="min_upper_edge_dist" value="0.0"/>
21124 <param name="extra_rt_extraction_window" value="0.0"/>
21125 <param name="mz_extraction_window_unit" value="Th"/>
21126 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21127 <param name="use_ms1_ion_mobility" value="false"/>
21128 <param name="matching_window_only" value="false"/>
21129 <param name="irt_mz_extraction_window" value="0.05"/>
21130 <param name="irt_mz_extraction_window_unit" value="Th"/>
21131 <param name="irt_im_extraction_window" value="-1.0"/>
21132 <param name="min_rsq" value="0.95"/>
21133 <param name="min_coverage" value="0.6"/>
21134 <param name="split_file_input" value="false"/>
21135 <param name="use_elution_model_score" value="false"/>
21136 <param name="readOptions" value="cache"/>
21137 <param name="mz_correction_function" value="none"/>
21138 <param name="extraction_function" value="tophat"/>
21139 <param name="batchSize" value="250"/>
21140 <param name="ms1_isotopes" value="0"/>
21141 <param name="force" value="false"/>
21142 <param name="test" value="true"/>
21143 </conditional>
21144 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21145 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21146 <param name="tr_type" value=""/>
21147 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21148 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21149 <param name="sonar" value="false"/>
21150 <param name="rt_extraction_window" value="600.0"/>
21151 <param name="ion_mobility_window" value="0.05"/>
21152 <param name="mz_extraction_window" value="0.05"/>
21153 <param name="mz_extraction_window_ms1" value="0.05"/>
21154 <param name="im_extraction_window_ms1" value="-1.0"/>
21155 <section name="Debugging"/>
21156 <section name="Calibration">
21157 <param name="ms1_im_calibration" value="false"/>
21158 <param name="im_correction_function" value="linear"/>
21159 <param name="debug_im_file" value=""/>
21160 <param name="debug_mz_file" value=""/>
21161 </section>
21162 <section name="Library">
21163 <param name="retentionTimeInterpretation" value="iRT"/>
21164 <param name="override_group_label_check" value="false"/>
21165 <param name="force_invalid_mods" value="false"/>
21166 </section>
21167 <section name="RTNormalization">
21168 <param name="alignmentMethod" value="linear"/>
21169 <param name="outlierMethod" value="iter_residual"/>
21170 <param name="useIterativeChauvenet" value="false"/>
21171 <param name="RANSACMaxIterations" value="1000"/>
21172 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21173 <param name="RANSACSamplingSize" value="10"/>
21174 <param name="estimateBestPeptides" value="false"/>
21175 <param name="InitialQualityCutoff" value="0.5"/>
21176 <param name="OverallQualityCutoff" value="5.5"/>
21177 <param name="NrRTBins" value="10"/>
21178 <param name="MinPeptidesPerBin" value="1"/>
21179 <param name="MinBinsFilled" value="8"/>
21180 <section name="lowess">
21181 <param name="span" value="0.666666666666667"/>
21182 </section>
21183 <section name="b_spline">
21184 <param name="num_nodes" value="5"/>
21185 </section>
21186 </section>
21187 <section name="Scoring">
21188 <param name="stop_report_after_feature" value="5"/>
21189 <param name="rt_normalization_factor" value="100.0"/>
21190 <param name="quantification_cutoff" value="0.0"/>
21191 <param name="write_convex_hull" value="false"/>
21192 <param name="spectrum_addition_method" value="simple"/>
21193 <param name="add_up_spectra" value="1"/>
21194 <param name="spacing_for_spectra_resampling" value="0.005"/>
21195 <param name="uis_threshold_sn" value="0"/>
21196 <param name="uis_threshold_peak_area" value="0"/>
21197 <param name="scoring_model" value="default"/>
21198 <param name="im_extra_drift" value="0.0"/>
21199 <section name="TransitionGroupPicker">
21200 <param name="stop_after_feature" value="-1"/>
21201 <param name="min_peak_width" value="-1.0"/>
21202 <param name="peak_integration" value="original"/>
21203 <param name="background_subtraction" value="none"/>
21204 <param name="recalculate_peaks" value="true"/>
21205 <param name="use_precursors" value="false"/>
21206 <param name="use_consensus" value="true"/>
21207 <param name="recalculate_peaks_max_z" value="0.75"/>
21208 <param name="minimal_quality" value="-1.5"/>
21209 <param name="resample_boundary" value="15.0"/>
21210 <param name="compute_peak_quality" value="true"/>
21211 <param name="compute_peak_shape_metrics" value="false"/>
21212 <param name="compute_total_mi" value="false"/>
21213 <param name="boundary_selection_method" value="largest"/>
21214 <section name="PeakPickerMRM">
21215 <param name="sgolay_frame_length" value="11"/>
21216 <param name="sgolay_polynomial_order" value="3"/>
21217 <param name="gauss_width" value="30.0"/>
21218 <param name="use_gauss" value="false"/>
21219 <param name="peak_width" value="-1.0"/>
21220 <param name="signal_to_noise" value="0.1"/>
21221 <param name="write_sn_log_messages" value="false"/>
21222 <param name="remove_overlapping_peaks" value="true"/>
21223 <param name="method" value="corrected"/>
21224 </section>
21225 <section name="PeakIntegrator">
21226 <param name="integration_type" value="intensity_sum"/>
21227 <param name="baseline_type" value="base_to_base"/>
21228 <param name="fit_EMG" value="false"/>
21229 </section>
21230 </section>
21231 <section name="DIAScoring">
21232 <param name="dia_extraction_window" value="0.05"/>
21233 <param name="dia_extraction_unit" value="Th"/>
21234 <param name="dia_centroided" value="false"/>
21235 <param name="dia_byseries_intensity_min" value="300.0"/>
21236 <param name="dia_byseries_ppm_diff" value="10.0"/>
21237 <param name="dia_nr_isotopes" value="4"/>
21238 <param name="dia_nr_charges" value="4"/>
21239 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21240 </section>
21241 <section name="EMGScoring">
21242 <param name="max_iteration" value="10"/>
21243 </section>
21244 <section name="Scores">
21245 <param name="use_shape_score" value="true"/>
21246 <param name="use_coelution_score" value="true"/>
21247 <param name="use_rt_score" value="true"/>
21248 <param name="use_library_score" value="true"/>
21249 <param name="use_intensity_score" value="true"/>
21250 <param name="use_nr_peaks_score" value="true"/>
21251 <param name="use_total_xic_score" value="true"/>
21252 <param name="use_total_mi_score" value="false"/>
21253 <param name="use_sn_score" value="true"/>
21254 <param name="use_mi_score" value="false"/>
21255 <param name="use_dia_scores" value="true"/>
21256 <param name="use_ms1_correlation" value="false"/>
21257 <param name="use_sonar_scores" value="false"/>
21258 <param name="use_ion_mobility_scores" value="true"/>
21259 <param name="use_ms1_fullscan" value="false"/>
21260 <param name="use_ms1_mi" value="false"/>
21261 <param name="use_uis_scores" value="false"/>
21262 </section>
21263 </section>
21264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21265 <output name="ctd_out" ftype="xml">
21266 <assert_contents>
21267 <is_valid_xml/>
21268 </assert_contents>
21269 </output>
21270 </test>
21271 <test expect_num_outputs="3">
21272 <conditional name="adv_opts_cond">
21273 <param name="adv_opts_selector" value="advanced"/>
21274 <param name="sort_swath_maps" value="false"/>
21275 <param name="use_ms1_traces" value="true"/>
21276 <param name="enable_uis_scoring" value="false"/>
21277 <param name="out_chrom_type" value="mzML"/>
21278 <param name="min_upper_edge_dist" value="0.0"/>
21279 <param name="extra_rt_extraction_window" value="0.0"/>
21280 <param name="mz_extraction_window_unit" value="Th"/>
21281 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21282 <param name="use_ms1_ion_mobility" value="false"/>
21283 <param name="matching_window_only" value="false"/>
21284 <param name="irt_mz_extraction_window" value="0.05"/>
21285 <param name="irt_mz_extraction_window_unit" value="Th"/>
21286 <param name="irt_im_extraction_window" value="-1.0"/>
21287 <param name="min_rsq" value="0.95"/>
21288 <param name="min_coverage" value="0.6"/>
21289 <param name="split_file_input" value="false"/>
21290 <param name="use_elution_model_score" value="false"/>
21291 <param name="readOptions" value="workingInMemory"/>
21292 <param name="mz_correction_function" value="none"/>
21293 <param name="extraction_function" value="tophat"/>
21294 <param name="batchSize" value="250"/>
21295 <param name="ms1_isotopes" value="0"/>
21296 <param name="force" value="false"/>
21297 <param name="test" value="true"/>
21298 </conditional>
21299 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21300 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
21301 <param name="tr_type" value="pqp"/>
21302 <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21303 <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21304 <param name="sonar" value="false"/>
21305 <param name="rt_extraction_window" value="600.0"/>
21306 <param name="ion_mobility_window" value="0.05"/>
21307 <param name="mz_extraction_window" value="0.05"/>
21308 <param name="mz_extraction_window_ms1" value="0.05"/>
21309 <param name="im_extraction_window_ms1" value="-1.0"/>
21310 <section name="Debugging"/>
21311 <section name="Calibration">
21312 <param name="ms1_im_calibration" value="false"/>
21313 <param name="im_correction_function" value="linear"/>
21314 <param name="debug_im_file" value=""/>
21315 <param name="debug_mz_file" value=""/>
21316 </section>
21317 <section name="Library">
21318 <param name="retentionTimeInterpretation" value="iRT"/>
21319 <param name="override_group_label_check" value="false"/>
21320 <param name="force_invalid_mods" value="false"/>
21321 </section>
21322 <section name="RTNormalization">
21323 <param name="alignmentMethod" value="linear"/>
21324 <param name="outlierMethod" value="iter_residual"/>
21325 <param name="useIterativeChauvenet" value="false"/>
21326 <param name="RANSACMaxIterations" value="1000"/>
21327 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21328 <param name="RANSACSamplingSize" value="10"/>
21329 <param name="estimateBestPeptides" value="false"/>
21330 <param name="InitialQualityCutoff" value="0.5"/>
21331 <param name="OverallQualityCutoff" value="5.5"/>
21332 <param name="NrRTBins" value="10"/>
21333 <param name="MinPeptidesPerBin" value="1"/>
21334 <param name="MinBinsFilled" value="8"/>
21335 <section name="lowess">
21336 <param name="span" value="0.666666666666667"/>
21337 </section>
21338 <section name="b_spline">
21339 <param name="num_nodes" value="5"/>
21340 </section>
21341 </section>
21342 <section name="Scoring">
21343 <param name="stop_report_after_feature" value="5"/>
21344 <param name="rt_normalization_factor" value="100.0"/>
21345 <param name="quantification_cutoff" value="0.0"/>
21346 <param name="write_convex_hull" value="false"/>
21347 <param name="spectrum_addition_method" value="simple"/>
21348 <param name="add_up_spectra" value="1"/>
21349 <param name="spacing_for_spectra_resampling" value="0.005"/>
21350 <param name="uis_threshold_sn" value="0"/>
21351 <param name="uis_threshold_peak_area" value="0"/>
21352 <param name="scoring_model" value="default"/>
21353 <param name="im_extra_drift" value="0.0"/>
21354 <section name="TransitionGroupPicker">
21355 <param name="stop_after_feature" value="-1"/>
21356 <param name="min_peak_width" value="-1.0"/>
21357 <param name="peak_integration" value="original"/>
21358 <param name="background_subtraction" value="none"/>
21359 <param name="recalculate_peaks" value="true"/>
21360 <param name="use_precursors" value="false"/>
21361 <param name="use_consensus" value="true"/>
21362 <param name="recalculate_peaks_max_z" value="0.75"/>
21363 <param name="minimal_quality" value="-1.5"/>
21364 <param name="resample_boundary" value="15.0"/>
21365 <param name="compute_peak_quality" value="true"/>
21366 <param name="compute_peak_shape_metrics" value="false"/>
21367 <param name="compute_total_mi" value="false"/>
21368 <param name="boundary_selection_method" value="largest"/>
21369 <section name="PeakPickerMRM">
21370 <param name="sgolay_frame_length" value="11"/>
21371 <param name="sgolay_polynomial_order" value="3"/>
21372 <param name="gauss_width" value="30.0"/>
21373 <param name="use_gauss" value="false"/>
21374 <param name="peak_width" value="-1.0"/>
21375 <param name="signal_to_noise" value="0.1"/>
21376 <param name="write_sn_log_messages" value="false"/>
21377 <param name="remove_overlapping_peaks" value="true"/>
21378 <param name="method" value="corrected"/>
21379 </section>
21380 <section name="PeakIntegrator">
21381 <param name="integration_type" value="intensity_sum"/>
21382 <param name="baseline_type" value="base_to_base"/>
21383 <param name="fit_EMG" value="false"/>
21384 </section>
21385 </section>
21386 <section name="DIAScoring">
21387 <param name="dia_extraction_window" value="0.05"/>
21388 <param name="dia_extraction_unit" value="Th"/>
21389 <param name="dia_centroided" value="false"/>
21390 <param name="dia_byseries_intensity_min" value="300.0"/>
21391 <param name="dia_byseries_ppm_diff" value="10.0"/>
21392 <param name="dia_nr_isotopes" value="4"/>
21393 <param name="dia_nr_charges" value="4"/>
21394 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21395 </section>
21396 <section name="EMGScoring">
21397 <param name="max_iteration" value="10"/>
21398 </section>
21399 <section name="Scores">
21400 <param name="use_shape_score" value="true"/>
21401 <param name="use_coelution_score" value="true"/>
21402 <param name="use_rt_score" value="true"/>
21403 <param name="use_library_score" value="true"/>
21404 <param name="use_intensity_score" value="true"/>
21405 <param name="use_nr_peaks_score" value="true"/>
21406 <param name="use_total_xic_score" value="true"/>
21407 <param name="use_total_mi_score" value="false"/>
21408 <param name="use_sn_score" value="true"/>
21409 <param name="use_mi_score" value="false"/>
21410 <param name="use_dia_scores" value="true"/>
21411 <param name="use_ms1_correlation" value="false"/>
21412 <param name="use_sonar_scores" value="false"/>
21413 <param name="use_ion_mobility_scores" value="false"/>
21414 <param name="use_ms1_fullscan" value="false"/>
21415 <param name="use_ms1_mi" value="false"/>
21416 <param name="use_uis_scores" value="false"/>
21417 </section>
21418 </section>
21419 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21420 <output name="ctd_out" ftype="xml">
21421 <assert_contents>
21422 <is_valid_xml/>
21423 </assert_contents>
21424 </output>
21425 </test>
21426 <test expect_num_outputs="2">
21427 <conditional name="adv_opts_cond">
21428 <param name="adv_opts_selector" value="advanced"/>
21429 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21430 <param name="sort_swath_maps" value="false"/>
21431 <param name="use_ms1_traces" value="true"/>
21432 <param name="enable_uis_scoring" value="false"/>
21433 <param name="min_upper_edge_dist" value="0.0"/>
21434 <param name="extra_rt_extraction_window" value="0.0"/>
21435 <param name="mz_extraction_window_unit" value="Th"/>
21436 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21437 <param name="use_ms1_ion_mobility" value="true"/>
21438 <param name="matching_window_only" value="false"/>
21439 <param name="irt_mz_extraction_window" value="0.05"/>
21440 <param name="irt_mz_extraction_window_unit" value="Th"/>
21441 <param name="irt_im_extraction_window" value="-1.0"/>
21442 <param name="min_rsq" value="0.95"/>
21443 <param name="min_coverage" value="0.6"/>
21444 <param name="split_file_input" value="false"/>
21445 <param name="use_elution_model_score" value="false"/>
21446 <param name="readOptions" value="normal"/>
21447 <param name="mz_correction_function" value="none"/>
21448 <param name="extraction_function" value="tophat"/>
21449 <param name="batchSize" value="250"/>
21450 <param name="ms1_isotopes" value="0"/>
21451 <param name="force" value="false"/>
21452 <param name="test" value="true"/>
21453 </conditional>
21454 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21455 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21456 <param name="tr_type" value=""/>
21457 <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21458 <param name="sonar" value="false"/>
21459 <param name="rt_extraction_window" value="600.0"/>
21460 <param name="ion_mobility_window" value="-1.0"/>
21461 <param name="mz_extraction_window" value="0.05"/>
21462 <param name="mz_extraction_window_ms1" value="0.05"/>
21463 <param name="im_extraction_window_ms1" value="-1.0"/>
21464 <section name="Debugging"/>
21465 <section name="Calibration">
21466 <param name="ms1_im_calibration" value="false"/>
21467 <param name="im_correction_function" value="linear"/>
21468 <param name="debug_im_file" value=""/>
21469 <param name="debug_mz_file" value=""/>
21470 </section>
21471 <section name="Library">
21472 <param name="retentionTimeInterpretation" value="iRT"/>
21473 <param name="override_group_label_check" value="false"/>
21474 <param name="force_invalid_mods" value="false"/>
21475 </section>
21476 <section name="RTNormalization">
21477 <param name="alignmentMethod" value="linear"/>
21478 <param name="outlierMethod" value="iter_residual"/>
21479 <param name="useIterativeChauvenet" value="false"/>
21480 <param name="RANSACMaxIterations" value="1000"/>
21481 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21482 <param name="RANSACSamplingSize" value="10"/>
21483 <param name="estimateBestPeptides" value="false"/>
21484 <param name="InitialQualityCutoff" value="0.5"/>
21485 <param name="OverallQualityCutoff" value="5.5"/>
21486 <param name="NrRTBins" value="10"/>
21487 <param name="MinPeptidesPerBin" value="1"/>
21488 <param name="MinBinsFilled" value="8"/>
21489 <section name="lowess">
21490 <param name="span" value="0.666666666666667"/>
21491 </section>
21492 <section name="b_spline">
21493 <param name="num_nodes" value="5"/>
21494 </section>
21495 </section>
21496 <section name="Scoring">
21497 <param name="stop_report_after_feature" value="5"/>
21498 <param name="rt_normalization_factor" value="100.0"/>
21499 <param name="quantification_cutoff" value="0.0"/>
21500 <param name="write_convex_hull" value="false"/>
21501 <param name="spectrum_addition_method" value="simple"/>
21502 <param name="add_up_spectra" value="1"/>
21503 <param name="spacing_for_spectra_resampling" value="0.005"/>
21504 <param name="uis_threshold_sn" value="0"/>
21505 <param name="uis_threshold_peak_area" value="0"/>
21506 <param name="scoring_model" value="default"/>
21507 <param name="im_extra_drift" value="0.0"/>
21508 <section name="TransitionGroupPicker">
21509 <param name="stop_after_feature" value="-1"/>
21510 <param name="min_peak_width" value="-1.0"/>
21511 <param name="peak_integration" value="original"/>
21512 <param name="background_subtraction" value="none"/>
21513 <param name="recalculate_peaks" value="true"/>
21514 <param name="use_precursors" value="false"/>
21515 <param name="use_consensus" value="true"/>
21516 <param name="recalculate_peaks_max_z" value="0.75"/>
21517 <param name="minimal_quality" value="-1.5"/>
21518 <param name="resample_boundary" value="15.0"/>
21519 <param name="compute_peak_quality" value="true"/>
21520 <param name="compute_peak_shape_metrics" value="false"/>
21521 <param name="compute_total_mi" value="false"/>
21522 <param name="boundary_selection_method" value="largest"/>
21523 <section name="PeakPickerMRM">
21524 <param name="sgolay_frame_length" value="11"/>
21525 <param name="sgolay_polynomial_order" value="3"/>
21526 <param name="gauss_width" value="30.0"/>
21527 <param name="use_gauss" value="false"/>
21528 <param name="peak_width" value="-1.0"/>
21529 <param name="signal_to_noise" value="0.1"/>
21530 <param name="write_sn_log_messages" value="false"/>
21531 <param name="remove_overlapping_peaks" value="true"/>
21532 <param name="method" value="corrected"/>
21533 </section>
21534 <section name="PeakIntegrator">
21535 <param name="integration_type" value="intensity_sum"/>
21536 <param name="baseline_type" value="base_to_base"/>
21537 <param name="fit_EMG" value="false"/>
21538 </section>
21539 </section>
21540 <section name="DIAScoring">
21541 <param name="dia_extraction_window" value="0.05"/>
21542 <param name="dia_extraction_unit" value="Th"/>
21543 <param name="dia_centroided" value="false"/>
21544 <param name="dia_byseries_intensity_min" value="300.0"/>
21545 <param name="dia_byseries_ppm_diff" value="10.0"/>
21546 <param name="dia_nr_isotopes" value="4"/>
21547 <param name="dia_nr_charges" value="4"/>
21548 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21549 </section>
21550 <section name="EMGScoring">
21551 <param name="max_iteration" value="10"/>
21552 </section>
21553 <section name="Scores">
21554 <param name="use_shape_score" value="true"/>
21555 <param name="use_coelution_score" value="true"/>
21556 <param name="use_rt_score" value="true"/>
21557 <param name="use_library_score" value="true"/>
21558 <param name="use_intensity_score" value="true"/>
21559 <param name="use_nr_peaks_score" value="true"/>
21560 <param name="use_total_xic_score" value="true"/>
21561 <param name="use_total_mi_score" value="false"/>
21562 <param name="use_sn_score" value="true"/>
21563 <param name="use_mi_score" value="false"/>
21564 <param name="use_dia_scores" value="true"/> 23026 <param name="use_dia_scores" value="true"/>
21565 <param name="use_ms1_correlation" value="false"/> 23027 <param name="use_ms1_correlation" value="false"/>
21566 <param name="use_sonar_scores" value="false"/> 23028 <param name="use_sonar_scores" value="false"/>
21567 <param name="use_ion_mobility_scores" value="false"/> 23029 <param name="use_ion_mobility_scores" value="false"/>
21568 <param name="use_ms1_fullscan" value="false"/> 23030 <param name="use_ms1_fullscan" value="false"/>
21569 <param name="use_ms1_mi" value="true"/> 23031 <param name="use_ms1_mi" value="true"/>
21570 <param name="use_uis_scores" value="false"/> 23032 <param name="use_uis_scores" value="false"/>
21571 </section> 23033 </section>
21572 </section> 23034 </section>
21573 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21574 <output name="ctd_out" ftype="xml">
21575 <assert_contents>
21576 <is_valid_xml/>
21577 </assert_contents>
21578 </output>
21579 </test>
21580 <test expect_num_outputs="2">
21581 <conditional name="adv_opts_cond">
21582 <param name="adv_opts_selector" value="advanced"/>
21583 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21584 <param name="sort_swath_maps" value="false"/>
21585 <param name="use_ms1_traces" value="true"/>
21586 <param name="enable_uis_scoring" value="false"/>
21587 <param name="min_upper_edge_dist" value="0.0"/>
21588 <param name="extra_rt_extraction_window" value="0.0"/>
21589 <param name="mz_extraction_window_unit" value="Th"/>
21590 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21591 <param name="use_ms1_ion_mobility" value="true"/>
21592 <param name="matching_window_only" value="false"/>
21593 <param name="irt_mz_extraction_window" value="0.05"/>
21594 <param name="irt_mz_extraction_window_unit" value="Th"/>
21595 <param name="irt_im_extraction_window" value="-1.0"/>
21596 <param name="min_rsq" value="0.95"/>
21597 <param name="min_coverage" value="0.6"/>
21598 <param name="split_file_input" value="false"/>
21599 <param name="use_elution_model_score" value="false"/>
21600 <param name="readOptions" value="normal"/>
21601 <param name="mz_correction_function" value="none"/>
21602 <param name="extraction_function" value="tophat"/>
21603 <param name="batchSize" value="250"/>
21604 <param name="ms1_isotopes" value="0"/>
21605 <param name="force" value="false"/>
21606 <param name="test" value="true"/>
21607 </conditional>
21608 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21609 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21610 <param name="tr_type" value=""/>
21611 <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21612 <param name="sonar" value="false"/>
21613 <param name="rt_extraction_window" value="600.0"/>
21614 <param name="ion_mobility_window" value="-1.0"/>
21615 <param name="mz_extraction_window" value="0.05"/>
21616 <param name="mz_extraction_window_ms1" value="0.05"/>
21617 <param name="im_extraction_window_ms1" value="-1.0"/>
21618 <section name="Debugging"/>
21619 <section name="Calibration">
21620 <param name="ms1_im_calibration" value="false"/>
21621 <param name="im_correction_function" value="linear"/>
21622 <param name="debug_im_file" value=""/>
21623 <param name="debug_mz_file" value=""/>
21624 </section>
21625 <section name="Library">
21626 <param name="retentionTimeInterpretation" value="iRT"/>
21627 <param name="override_group_label_check" value="false"/>
21628 <param name="force_invalid_mods" value="false"/>
21629 </section>
21630 <section name="RTNormalization">
21631 <param name="alignmentMethod" value="linear"/>
21632 <param name="outlierMethod" value="iter_residual"/>
21633 <param name="useIterativeChauvenet" value="false"/>
21634 <param name="RANSACMaxIterations" value="1000"/>
21635 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21636 <param name="RANSACSamplingSize" value="10"/>
21637 <param name="estimateBestPeptides" value="false"/>
21638 <param name="InitialQualityCutoff" value="0.5"/>
21639 <param name="OverallQualityCutoff" value="5.5"/>
21640 <param name="NrRTBins" value="10"/>
21641 <param name="MinPeptidesPerBin" value="1"/>
21642 <param name="MinBinsFilled" value="8"/>
21643 <section name="lowess">
21644 <param name="span" value="0.666666666666667"/>
21645 </section>
21646 <section name="b_spline">
21647 <param name="num_nodes" value="5"/>
21648 </section>
21649 </section>
21650 <section name="Scoring">
21651 <param name="stop_report_after_feature" value="5"/>
21652 <param name="rt_normalization_factor" value="100.0"/>
21653 <param name="quantification_cutoff" value="0.0"/>
21654 <param name="write_convex_hull" value="false"/>
21655 <param name="spectrum_addition_method" value="simple"/>
21656 <param name="add_up_spectra" value="1"/>
21657 <param name="spacing_for_spectra_resampling" value="0.005"/>
21658 <param name="uis_threshold_sn" value="0"/>
21659 <param name="uis_threshold_peak_area" value="0"/>
21660 <param name="scoring_model" value="default"/>
21661 <param name="im_extra_drift" value="0.0"/>
21662 <section name="TransitionGroupPicker">
21663 <param name="stop_after_feature" value="-1"/>
21664 <param name="min_peak_width" value="-1.0"/>
21665 <param name="peak_integration" value="original"/>
21666 <param name="background_subtraction" value="none"/>
21667 <param name="recalculate_peaks" value="true"/>
21668 <param name="use_precursors" value="false"/>
21669 <param name="use_consensus" value="true"/>
21670 <param name="recalculate_peaks_max_z" value="0.75"/>
21671 <param name="minimal_quality" value="-1.5"/>
21672 <param name="resample_boundary" value="15.0"/>
21673 <param name="compute_peak_quality" value="true"/>
21674 <param name="compute_peak_shape_metrics" value="false"/>
21675 <param name="compute_total_mi" value="false"/>
21676 <param name="boundary_selection_method" value="largest"/>
21677 <section name="PeakPickerMRM">
21678 <param name="sgolay_frame_length" value="11"/>
21679 <param name="sgolay_polynomial_order" value="3"/>
21680 <param name="gauss_width" value="30.0"/>
21681 <param name="use_gauss" value="false"/>
21682 <param name="peak_width" value="-1.0"/>
21683 <param name="signal_to_noise" value="0.1"/>
21684 <param name="write_sn_log_messages" value="false"/>
21685 <param name="remove_overlapping_peaks" value="true"/>
21686 <param name="method" value="corrected"/>
21687 </section>
21688 <section name="PeakIntegrator">
21689 <param name="integration_type" value="intensity_sum"/>
21690 <param name="baseline_type" value="base_to_base"/>
21691 <param name="fit_EMG" value="false"/>
21692 </section>
21693 </section>
21694 <section name="DIAScoring">
21695 <param name="dia_extraction_window" value="0.05"/>
21696 <param name="dia_extraction_unit" value="Th"/>
21697 <param name="dia_centroided" value="false"/>
21698 <param name="dia_byseries_intensity_min" value="300.0"/>
21699 <param name="dia_byseries_ppm_diff" value="10.0"/>
21700 <param name="dia_nr_isotopes" value="4"/>
21701 <param name="dia_nr_charges" value="4"/>
21702 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21703 </section>
21704 <section name="EMGScoring">
21705 <param name="max_iteration" value="10"/>
21706 </section>
21707 <section name="Scores">
21708 <param name="use_shape_score" value="true"/>
21709 <param name="use_coelution_score" value="true"/>
21710 <param name="use_rt_score" value="true"/>
21711 <param name="use_library_score" value="true"/>
21712 <param name="use_intensity_score" value="true"/>
21713 <param name="use_nr_peaks_score" value="true"/>
21714 <param name="use_total_xic_score" value="true"/>
21715 <param name="use_total_mi_score" value="false"/>
21716 <param name="use_sn_score" value="true"/>
21717 <param name="use_mi_score" value="true"/>
21718 <param name="use_dia_scores" value="true"/>
21719 <param name="use_ms1_correlation" value="false"/>
21720 <param name="use_sonar_scores" value="false"/>
21721 <param name="use_ion_mobility_scores" value="false"/>
21722 <param name="use_ms1_fullscan" value="false"/>
21723 <param name="use_ms1_mi" value="false"/>
21724 <param name="use_uis_scores" value="false"/>
21725 </section>
21726 </section>
21727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21728 <output name="ctd_out" ftype="xml">
21729 <assert_contents>
21730 <is_valid_xml/>
21731 </assert_contents>
21732 </output>
21733 </test>
21734 <test expect_num_outputs="2">
21735 <conditional name="adv_opts_cond">
21736 <param name="adv_opts_selector" value="advanced"/>
21737 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21738 <param name="sort_swath_maps" value="false"/>
21739 <param name="use_ms1_traces" value="true"/>
21740 <param name="enable_uis_scoring" value="false"/>
21741 <param name="min_upper_edge_dist" value="0.0"/>
21742 <param name="extra_rt_extraction_window" value="0.0"/>
21743 <param name="mz_extraction_window_unit" value="Th"/>
21744 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21745 <param name="use_ms1_ion_mobility" value="true"/>
21746 <param name="matching_window_only" value="false"/>
21747 <param name="irt_mz_extraction_window" value="0.05"/>
21748 <param name="irt_mz_extraction_window_unit" value="Th"/>
21749 <param name="irt_im_extraction_window" value="-1.0"/>
21750 <param name="min_rsq" value="0.95"/>
21751 <param name="min_coverage" value="0.6"/>
21752 <param name="split_file_input" value="false"/>
21753 <param name="use_elution_model_score" value="false"/>
21754 <param name="readOptions" value="normal"/>
21755 <param name="mz_correction_function" value="none"/>
21756 <param name="extraction_function" value="tophat"/>
21757 <param name="batchSize" value="250"/>
21758 <param name="ms1_isotopes" value="0"/>
21759 <param name="force" value="false"/>
21760 <param name="test" value="true"/>
21761 </conditional>
21762 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21763 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21764 <param name="tr_type" value=""/>
21765 <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21766 <param name="sonar" value="false"/>
21767 <param name="rt_extraction_window" value="600.0"/>
21768 <param name="ion_mobility_window" value="-1.0"/>
21769 <param name="mz_extraction_window" value="0.05"/>
21770 <param name="mz_extraction_window_ms1" value="0.05"/>
21771 <param name="im_extraction_window_ms1" value="-1.0"/>
21772 <section name="Debugging"/>
21773 <section name="Calibration">
21774 <param name="ms1_im_calibration" value="false"/>
21775 <param name="im_correction_function" value="linear"/>
21776 <param name="debug_im_file" value=""/>
21777 <param name="debug_mz_file" value=""/>
21778 </section>
21779 <section name="Library">
21780 <param name="retentionTimeInterpretation" value="iRT"/>
21781 <param name="override_group_label_check" value="false"/>
21782 <param name="force_invalid_mods" value="false"/>
21783 </section>
21784 <section name="RTNormalization">
21785 <param name="alignmentMethod" value="linear"/>
21786 <param name="outlierMethod" value="iter_residual"/>
21787 <param name="useIterativeChauvenet" value="false"/>
21788 <param name="RANSACMaxIterations" value="1000"/>
21789 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21790 <param name="RANSACSamplingSize" value="10"/>
21791 <param name="estimateBestPeptides" value="false"/>
21792 <param name="InitialQualityCutoff" value="0.5"/>
21793 <param name="OverallQualityCutoff" value="5.5"/>
21794 <param name="NrRTBins" value="10"/>
21795 <param name="MinPeptidesPerBin" value="1"/>
21796 <param name="MinBinsFilled" value="8"/>
21797 <section name="lowess">
21798 <param name="span" value="0.666666666666667"/>
21799 </section>
21800 <section name="b_spline">
21801 <param name="num_nodes" value="5"/>
21802 </section>
21803 </section>
21804 <section name="Scoring">
21805 <param name="stop_report_after_feature" value="5"/>
21806 <param name="rt_normalization_factor" value="100.0"/>
21807 <param name="quantification_cutoff" value="0.0"/>
21808 <param name="write_convex_hull" value="false"/>
21809 <param name="spectrum_addition_method" value="simple"/>
21810 <param name="add_up_spectra" value="1"/>
21811 <param name="spacing_for_spectra_resampling" value="0.005"/>
21812 <param name="uis_threshold_sn" value="0"/>
21813 <param name="uis_threshold_peak_area" value="0"/>
21814 <param name="scoring_model" value="default"/>
21815 <param name="im_extra_drift" value="0.0"/>
21816 <section name="TransitionGroupPicker">
21817 <param name="stop_after_feature" value="-1"/>
21818 <param name="min_peak_width" value="-1.0"/>
21819 <param name="peak_integration" value="original"/>
21820 <param name="background_subtraction" value="none"/>
21821 <param name="recalculate_peaks" value="true"/>
21822 <param name="use_precursors" value="false"/>
21823 <param name="use_consensus" value="true"/>
21824 <param name="recalculate_peaks_max_z" value="0.75"/>
21825 <param name="minimal_quality" value="-1.5"/>
21826 <param name="resample_boundary" value="15.0"/>
21827 <param name="compute_peak_quality" value="true"/>
21828 <param name="compute_peak_shape_metrics" value="false"/>
21829 <param name="compute_total_mi" value="false"/>
21830 <param name="boundary_selection_method" value="largest"/>
21831 <section name="PeakPickerMRM">
21832 <param name="sgolay_frame_length" value="11"/>
21833 <param name="sgolay_polynomial_order" value="3"/>
21834 <param name="gauss_width" value="30.0"/>
21835 <param name="use_gauss" value="false"/>
21836 <param name="peak_width" value="-1.0"/>
21837 <param name="signal_to_noise" value="0.1"/>
21838 <param name="write_sn_log_messages" value="false"/>
21839 <param name="remove_overlapping_peaks" value="true"/>
21840 <param name="method" value="corrected"/>
21841 </section>
21842 <section name="PeakIntegrator">
21843 <param name="integration_type" value="intensity_sum"/>
21844 <param name="baseline_type" value="base_to_base"/>
21845 <param name="fit_EMG" value="false"/>
21846 </section>
21847 </section>
21848 <section name="DIAScoring">
21849 <param name="dia_extraction_window" value="0.05"/>
21850 <param name="dia_extraction_unit" value="Th"/>
21851 <param name="dia_centroided" value="false"/>
21852 <param name="dia_byseries_intensity_min" value="300.0"/>
21853 <param name="dia_byseries_ppm_diff" value="10.0"/>
21854 <param name="dia_nr_isotopes" value="4"/>
21855 <param name="dia_nr_charges" value="4"/>
21856 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21857 </section>
21858 <section name="EMGScoring">
21859 <param name="max_iteration" value="10"/>
21860 </section>
21861 <section name="Scores">
21862 <param name="use_shape_score" value="true"/>
21863 <param name="use_coelution_score" value="true"/>
21864 <param name="use_rt_score" value="true"/>
21865 <param name="use_library_score" value="true"/>
21866 <param name="use_intensity_score" value="true"/>
21867 <param name="use_nr_peaks_score" value="true"/>
21868 <param name="use_total_xic_score" value="true"/>
21869 <param name="use_total_mi_score" value="true"/>
21870 <param name="use_sn_score" value="true"/>
21871 <param name="use_mi_score" value="true"/>
21872 <param name="use_dia_scores" value="true"/>
21873 <param name="use_ms1_correlation" value="false"/>
21874 <param name="use_sonar_scores" value="false"/>
21875 <param name="use_ion_mobility_scores" value="false"/>
21876 <param name="use_ms1_fullscan" value="false"/>
21877 <param name="use_ms1_mi" value="false"/>
21878 <param name="use_uis_scores" value="false"/>
21879 </section>
21880 </section>
21881 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21882 <output name="ctd_out" ftype="xml">
21883 <assert_contents>
21884 <is_valid_xml/>
21885 </assert_contents>
21886 </output>
21887 </test>
21888 <test expect_num_outputs="4">
21889 <conditional name="adv_opts_cond">
21890 <param name="adv_opts_selector" value="advanced"/>
21891 <param name="sort_swath_maps" value="false"/>
21892 <param name="use_ms1_traces" value="true"/>
21893 <param name="enable_uis_scoring" value="false"/>
21894 <param name="out_chrom_type" value="mzML"/>
21895 <param name="min_upper_edge_dist" value="0.0"/>
21896 <param name="extra_rt_extraction_window" value="0.0"/>
21897 <param name="mz_extraction_window_unit" value="Th"/>
21898 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21899 <param name="use_ms1_ion_mobility" value="true"/>
21900 <param name="matching_window_only" value="false"/>
21901 <param name="irt_mz_extraction_window" value="0.05"/>
21902 <param name="irt_mz_extraction_window_unit" value="Th"/>
21903 <param name="irt_im_extraction_window" value="-1.0"/>
21904 <param name="min_rsq" value="0.95"/>
21905 <param name="min_coverage" value="0.6"/>
21906 <param name="split_file_input" value="false"/>
21907 <param name="use_elution_model_score" value="false"/>
21908 <param name="readOptions" value="normal"/>
21909 <param name="mz_correction_function" value="none"/>
21910 <param name="extraction_function" value="tophat"/>
21911 <param name="batchSize" value="250"/>
21912 <param name="ms1_isotopes" value="0"/>
21913 <param name="force" value="false"/>
21914 <param name="test" value="true"/>
21915 </conditional>
21916 <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
21917 <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
21918 <param name="tr_type" value=""/>
21919 <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
21920 <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21921 <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21922 <param name="sonar" value="false"/>
21923 <param name="rt_extraction_window" value="600.0"/>
21924 <param name="ion_mobility_window" value="-1.0"/>
21925 <param name="mz_extraction_window" value="0.05"/>
21926 <param name="mz_extraction_window_ms1" value="0.05"/>
21927 <param name="im_extraction_window_ms1" value="-1.0"/>
21928 <section name="Debugging"/>
21929 <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
21930 <section name="Calibration">
21931 <param name="ms1_im_calibration" value="false"/>
21932 <param name="im_correction_function" value="linear"/>
21933 <param name="debug_im_file" value=""/>
21934 <param name="debug_mz_file" value=""/>
21935 </section>
21936 <section name="Library">
21937 <param name="retentionTimeInterpretation" value="iRT"/>
21938 <param name="override_group_label_check" value="false"/>
21939 <param name="force_invalid_mods" value="false"/>
21940 </section>
21941 <section name="RTNormalization">
21942 <param name="alignmentMethod" value="linear"/>
21943 <param name="outlierMethod" value="iter_residual"/>
21944 <param name="useIterativeChauvenet" value="false"/>
21945 <param name="RANSACMaxIterations" value="1000"/>
21946 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21947 <param name="RANSACSamplingSize" value="10"/>
21948 <param name="estimateBestPeptides" value="false"/>
21949 <param name="InitialQualityCutoff" value="0.5"/>
21950 <param name="OverallQualityCutoff" value="5.5"/>
21951 <param name="NrRTBins" value="10"/>
21952 <param name="MinPeptidesPerBin" value="1"/>
21953 <param name="MinBinsFilled" value="8"/>
21954 <section name="lowess">
21955 <param name="span" value="0.666666666666667"/>
21956 </section>
21957 <section name="b_spline">
21958 <param name="num_nodes" value="5"/>
21959 </section>
21960 </section>
21961 <section name="Scoring">
21962 <param name="stop_report_after_feature" value="5"/>
21963 <param name="rt_normalization_factor" value="100.0"/>
21964 <param name="quantification_cutoff" value="0.0"/>
21965 <param name="write_convex_hull" value="false"/>
21966 <param name="spectrum_addition_method" value="simple"/>
21967 <param name="add_up_spectra" value="1"/>
21968 <param name="spacing_for_spectra_resampling" value="0.005"/>
21969 <param name="uis_threshold_sn" value="0"/>
21970 <param name="uis_threshold_peak_area" value="0"/>
21971 <param name="scoring_model" value="default"/>
21972 <param name="im_extra_drift" value="0.0"/>
21973 <section name="TransitionGroupPicker">
21974 <param name="stop_after_feature" value="-1"/>
21975 <param name="min_peak_width" value="-1.0"/>
21976 <param name="peak_integration" value="original"/>
21977 <param name="background_subtraction" value="none"/>
21978 <param name="recalculate_peaks" value="true"/>
21979 <param name="use_precursors" value="false"/>
21980 <param name="use_consensus" value="true"/>
21981 <param name="recalculate_peaks_max_z" value="0.75"/>
21982 <param name="minimal_quality" value="-1.5"/>
21983 <param name="resample_boundary" value="15.0"/>
21984 <param name="compute_peak_quality" value="true"/>
21985 <param name="compute_peak_shape_metrics" value="false"/>
21986 <param name="compute_total_mi" value="false"/>
21987 <param name="boundary_selection_method" value="largest"/>
21988 <section name="PeakPickerMRM">
21989 <param name="sgolay_frame_length" value="11"/>
21990 <param name="sgolay_polynomial_order" value="3"/>
21991 <param name="gauss_width" value="30.0"/>
21992 <param name="use_gauss" value="false"/>
21993 <param name="peak_width" value="-1.0"/>
21994 <param name="signal_to_noise" value="0.1"/>
21995 <param name="write_sn_log_messages" value="false"/>
21996 <param name="remove_overlapping_peaks" value="true"/>
21997 <param name="method" value="corrected"/>
21998 </section>
21999 <section name="PeakIntegrator">
22000 <param name="integration_type" value="intensity_sum"/>
22001 <param name="baseline_type" value="base_to_base"/>
22002 <param name="fit_EMG" value="false"/>
22003 </section>
22004 </section>
22005 <section name="DIAScoring">
22006 <param name="dia_extraction_window" value="0.05"/>
22007 <param name="dia_extraction_unit" value="Th"/>
22008 <param name="dia_centroided" value="false"/>
22009 <param name="dia_byseries_intensity_min" value="300.0"/>
22010 <param name="dia_byseries_ppm_diff" value="10.0"/>
22011 <param name="dia_nr_isotopes" value="4"/>
22012 <param name="dia_nr_charges" value="4"/>
22013 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22014 </section>
22015 <section name="EMGScoring">
22016 <param name="max_iteration" value="10"/>
22017 </section>
22018 <section name="Scores">
22019 <param name="use_shape_score" value="true"/>
22020 <param name="use_coelution_score" value="true"/>
22021 <param name="use_rt_score" value="true"/>
22022 <param name="use_library_score" value="true"/>
22023 <param name="use_intensity_score" value="true"/>
22024 <param name="use_nr_peaks_score" value="true"/>
22025 <param name="use_total_xic_score" value="true"/>
22026 <param name="use_total_mi_score" value="true"/>
22027 <param name="use_sn_score" value="true"/>
22028 <param name="use_mi_score" value="true"/>
22029 <param name="use_dia_scores" value="true"/>
22030 <param name="use_ms1_correlation" value="false"/>
22031 <param name="use_sonar_scores" value="false"/>
22032 <param name="use_ion_mobility_scores" value="false"/>
22033 <param name="use_ms1_fullscan" value="false"/>
22034 <param name="use_ms1_mi" value="false"/>
22035 <param name="use_uis_scores" value="false"/>
22036 </section>
22037 </section>
22038 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
22039 <output name="ctd_out" ftype="xml">
22040 <assert_contents>
22041 <is_valid_xml/>
22042 </assert_contents>
22043 </output>
22044 </test>
22045 <test expect_num_outputs="3">
22046 <conditional name="adv_opts_cond">
22047 <param name="adv_opts_selector" value="advanced"/>
22048 <param name="sort_swath_maps" value="false"/>
22049 <param name="use_ms1_traces" value="true"/>
22050 <param name="enable_uis_scoring" value="false"/>
22051 <param name="out_chrom_type" value="mzML"/>
22052 <param name="min_upper_edge_dist" value="0.0"/>
22053 <param name="extra_rt_extraction_window" value="0.0"/>
22054 <param name="mz_extraction_window_unit" value="Th"/>
22055 <param name="mz_extraction_window_ms1_unit" value="Th"/>
22056 <param name="use_ms1_ion_mobility" value="true"/>
22057 <param name="matching_window_only" value="true"/>
22058 <param name="irt_mz_extraction_window" value="0.05"/>
22059 <param name="irt_mz_extraction_window_unit" value="Th"/>
22060 <param name="irt_im_extraction_window" value="-1.0"/>
22061 <param name="min_rsq" value="0.95"/>
22062 <param name="min_coverage" value="0.6"/>
22063 <param name="split_file_input" value="false"/>
22064 <param name="use_elution_model_score" value="false"/>
22065 <param name="readOptions" value="workingInMemory"/>
22066 <param name="mz_correction_function" value="none"/>
22067 <param name="extraction_function" value="tophat"/>
22068 <param name="batchSize" value="250"/>
22069 <param name="ms1_isotopes" value="3"/>
22070 <param name="force" value="false"/>
22071 <param name="test" value="true"/>
22072 </conditional>
22073 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
22074 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
22075 <param name="tr_type" value=""/>
22076 <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22077 <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22078 <param name="sonar" value="false"/>
22079 <param name="rt_extraction_window" value="600.0"/>
22080 <param name="ion_mobility_window" value="-1.0"/>
22081 <param name="mz_extraction_window" value="0.05"/>
22082 <param name="mz_extraction_window_ms1" value="0.05"/>
22083 <param name="im_extraction_window_ms1" value="-1.0"/>
22084 <section name="Debugging"/>
22085 <section name="Calibration">
22086 <param name="ms1_im_calibration" value="false"/>
22087 <param name="im_correction_function" value="linear"/>
22088 <param name="debug_im_file" value=""/>
22089 <param name="debug_mz_file" value=""/>
22090 </section>
22091 <section name="Library">
22092 <param name="retentionTimeInterpretation" value="iRT"/>
22093 <param name="override_group_label_check" value="false"/>
22094 <param name="force_invalid_mods" value="false"/>
22095 </section>
22096 <section name="RTNormalization">
22097 <param name="alignmentMethod" value="linear"/>
22098 <param name="outlierMethod" value="iter_residual"/>
22099 <param name="useIterativeChauvenet" value="false"/>
22100 <param name="RANSACMaxIterations" value="1000"/>
22101 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22102 <param name="RANSACSamplingSize" value="10"/>
22103 <param name="estimateBestPeptides" value="false"/>
22104 <param name="InitialQualityCutoff" value="0.5"/>
22105 <param name="OverallQualityCutoff" value="5.5"/>
22106 <param name="NrRTBins" value="10"/>
22107 <param name="MinPeptidesPerBin" value="1"/>
22108 <param name="MinBinsFilled" value="8"/>
22109 <section name="lowess">
22110 <param name="span" value="0.666666666666667"/>
22111 </section>
22112 <section name="b_spline">
22113 <param name="num_nodes" value="5"/>
22114 </section>
22115 </section>
22116 <section name="Scoring">
22117 <param name="stop_report_after_feature" value="5"/>
22118 <param name="rt_normalization_factor" value="100.0"/>
22119 <param name="quantification_cutoff" value="0.0"/>
22120 <param name="write_convex_hull" value="false"/>
22121 <param name="spectrum_addition_method" value="simple"/>
22122 <param name="add_up_spectra" value="1"/>
22123 <param name="spacing_for_spectra_resampling" value="0.005"/>
22124 <param name="uis_threshold_sn" value="0"/>
22125 <param name="uis_threshold_peak_area" value="0"/>
22126 <param name="scoring_model" value="default"/>
22127 <param name="im_extra_drift" value="0.0"/>
22128 <section name="TransitionGroupPicker">
22129 <param name="stop_after_feature" value="-1"/>
22130 <param name="min_peak_width" value="-1.0"/>
22131 <param name="peak_integration" value="original"/>
22132 <param name="background_subtraction" value="none"/>
22133 <param name="recalculate_peaks" value="true"/>
22134 <param name="use_precursors" value="false"/>
22135 <param name="use_consensus" value="true"/>
22136 <param name="recalculate_peaks_max_z" value="0.75"/>
22137 <param name="minimal_quality" value="-1.5"/>
22138 <param name="resample_boundary" value="15.0"/>
22139 <param name="compute_peak_quality" value="true"/>
22140 <param name="compute_peak_shape_metrics" value="false"/>
22141 <param name="compute_total_mi" value="false"/>
22142 <param name="boundary_selection_method" value="largest"/>
22143 <section name="PeakPickerMRM">
22144 <param name="sgolay_frame_length" value="11"/>
22145 <param name="sgolay_polynomial_order" value="3"/>
22146 <param name="gauss_width" value="30.0"/>
22147 <param name="use_gauss" value="false"/>
22148 <param name="peak_width" value="-1.0"/>
22149 <param name="signal_to_noise" value="0.1"/>
22150 <param name="write_sn_log_messages" value="false"/>
22151 <param name="remove_overlapping_peaks" value="true"/>
22152 <param name="method" value="corrected"/>
22153 </section>
22154 <section name="PeakIntegrator">
22155 <param name="integration_type" value="intensity_sum"/>
22156 <param name="baseline_type" value="base_to_base"/>
22157 <param name="fit_EMG" value="false"/>
22158 </section>
22159 </section>
22160 <section name="DIAScoring">
22161 <param name="dia_extraction_window" value="0.05"/>
22162 <param name="dia_extraction_unit" value="Th"/>
22163 <param name="dia_centroided" value="false"/>
22164 <param name="dia_byseries_intensity_min" value="300.0"/>
22165 <param name="dia_byseries_ppm_diff" value="10.0"/>
22166 <param name="dia_nr_isotopes" value="4"/>
22167 <param name="dia_nr_charges" value="4"/>
22168 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22169 </section>
22170 <section name="EMGScoring">
22171 <param name="max_iteration" value="10"/>
22172 </section>
22173 <section name="Scores">
22174 <param name="use_shape_score" value="true"/>
22175 <param name="use_coelution_score" value="true"/>
22176 <param name="use_rt_score" value="true"/>
22177 <param name="use_library_score" value="true"/>
22178 <param name="use_intensity_score" value="true"/>
22179 <param name="use_nr_peaks_score" value="true"/>
22180 <param name="use_total_xic_score" value="true"/>
22181 <param name="use_total_mi_score" value="false"/>
22182 <param name="use_sn_score" value="true"/>
22183 <param name="use_mi_score" value="false"/>
22184 <param name="use_dia_scores" value="true"/>
22185 <param name="use_ms1_correlation" value="false"/>
22186 <param name="use_sonar_scores" value="false"/>
22187 <param name="use_ion_mobility_scores" value="false"/>
22188 <param name="use_ms1_fullscan" value="false"/>
22189 <param name="use_ms1_mi" value="false"/>
22190 <param name="use_uis_scores" value="false"/>
22191 </section>
22192 </section>
22193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> 23035 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22194 <output name="ctd_out" ftype="xml"> 23036 <output name="ctd_out" ftype="xml">
22195 <assert_contents> 23037 <assert_contents>
22196 <is_valid_xml/> 23038 <is_valid_xml/>
22197 </assert_contents> 23039 </assert_contents>
22205 <param name="processOption" value="inmemory"/> 23047 <param name="processOption" value="inmemory"/>
22206 <param name="force" value="false"/> 23048 <param name="force" value="false"/>
22207 <param name="test" value="true"/> 23049 <param name="test" value="true"/>
22208 </conditional> 23050 </conditional>
22209 <param name="in" value="PeakPickerHiRes_input.mzML"/> 23051 <param name="in" value="PeakPickerHiRes_input.mzML"/>
22210 <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/> 23052 <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22211 <section name="algorithm"> 23053 <section name="algorithm">
22212 <param name="signal_to_noise" value="1.0"/> 23054 <param name="signal_to_noise" value="1.0"/>
22213 <param name="spacing_difference_gap" value="4.0"/> 23055 <param name="spacing_difference_gap" value="4.0"/>
22214 <param name="spacing_difference" value="1.5"/> 23056 <param name="spacing_difference" value="1.5"/>
22215 <param name="missing" value="1"/> 23057 <param name="missing" value="1"/>
22760 <param name="decoy_string_position" value="prefix"/> 23602 <param name="decoy_string_position" value="prefix"/>
22761 <param name="missing_decoy_action" value="error"/> 23603 <param name="missing_decoy_action" value="error"/>
22762 <param name="write_protein_sequence" value="false"/> 23604 <param name="write_protein_sequence" value="false"/>
22763 <param name="write_protein_description" value="false"/> 23605 <param name="write_protein_description" value="false"/>
22764 <param name="keep_unreferenced_proteins" value="false"/> 23606 <param name="keep_unreferenced_proteins" value="false"/>
22765 <param name="allow_unmatched" value="true"/> 23607 <param name="unmatched_action" value="warn"/>
22766 <param name="aaa_max" value="4"/> 23608 <param name="aaa_max" value="4"/>
22767 <param name="mismatches_max" value="0"/> 23609 <param name="mismatches_max" value="0"/>
22768 <param name="IL_equivalent" value="false"/> 23610 <param name="IL_equivalent" value="false"/>
22769 <section name="enzyme"> 23611 <section name="enzyme">
22770 <param name="name" value="Trypsin"/> 23612 <param name="name" value="auto"/>
22771 <param name="specificity" value="none"/> 23613 <param name="specificity" value="none"/>
22772 </section> 23614 </section>
22773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23615 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22774 <output name="ctd_out" ftype="xml"> 23616 <output name="ctd_out" ftype="xml">
22775 <assert_contents> 23617 <assert_contents>
22790 <param name="decoy_string_position" value="prefix"/> 23632 <param name="decoy_string_position" value="prefix"/>
22791 <param name="missing_decoy_action" value="error"/> 23633 <param name="missing_decoy_action" value="error"/>
22792 <param name="write_protein_sequence" value="true"/> 23634 <param name="write_protein_sequence" value="true"/>
22793 <param name="write_protein_description" value="false"/> 23635 <param name="write_protein_description" value="false"/>
22794 <param name="keep_unreferenced_proteins" value="false"/> 23636 <param name="keep_unreferenced_proteins" value="false"/>
22795 <param name="allow_unmatched" value="true"/> 23637 <param name="unmatched_action" value="warn"/>
22796 <param name="aaa_max" value="4"/> 23638 <param name="aaa_max" value="4"/>
22797 <param name="mismatches_max" value="0"/> 23639 <param name="mismatches_max" value="0"/>
22798 <param name="IL_equivalent" value="false"/> 23640 <param name="IL_equivalent" value="false"/>
22799 <section name="enzyme"> 23641 <section name="enzyme">
22800 <param name="name" value="Trypsin"/> 23642 <param name="name" value="auto"/>
22801 <param name="specificity" value="none"/> 23643 <param name="specificity" value="none"/>
22802 </section> 23644 </section>
22803 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23645 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22804 <output name="ctd_out" ftype="xml"> 23646 <output name="ctd_out" ftype="xml">
22805 <assert_contents> 23647 <assert_contents>
22820 <param name="decoy_string_position" value="prefix"/> 23662 <param name="decoy_string_position" value="prefix"/>
22821 <param name="missing_decoy_action" value="error"/> 23663 <param name="missing_decoy_action" value="error"/>
22822 <param name="write_protein_sequence" value="false"/> 23664 <param name="write_protein_sequence" value="false"/>
22823 <param name="write_protein_description" value="false"/> 23665 <param name="write_protein_description" value="false"/>
22824 <param name="keep_unreferenced_proteins" value="true"/> 23666 <param name="keep_unreferenced_proteins" value="true"/>
22825 <param name="allow_unmatched" value="true"/> 23667 <param name="unmatched_action" value="warn"/>
22826 <param name="aaa_max" value="4"/> 23668 <param name="aaa_max" value="4"/>
22827 <param name="mismatches_max" value="0"/> 23669 <param name="mismatches_max" value="0"/>
22828 <param name="IL_equivalent" value="false"/> 23670 <param name="IL_equivalent" value="false"/>
22829 <section name="enzyme"> 23671 <section name="enzyme">
22830 <param name="name" value="Trypsin"/> 23672 <param name="name" value="auto"/>
22831 <param name="specificity" value="none"/> 23673 <param name="specificity" value="none"/>
22832 </section> 23674 </section>
22833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22834 <output name="ctd_out" ftype="xml"> 23676 <output name="ctd_out" ftype="xml">
22835 <assert_contents> 23677 <assert_contents>
22850 <param name="decoy_string_position" value="prefix"/> 23692 <param name="decoy_string_position" value="prefix"/>
22851 <param name="missing_decoy_action" value="error"/> 23693 <param name="missing_decoy_action" value="error"/>
22852 <param name="write_protein_sequence" value="true"/> 23694 <param name="write_protein_sequence" value="true"/>
22853 <param name="write_protein_description" value="false"/> 23695 <param name="write_protein_description" value="false"/>
22854 <param name="keep_unreferenced_proteins" value="false"/> 23696 <param name="keep_unreferenced_proteins" value="false"/>
22855 <param name="allow_unmatched" value="true"/> 23697 <param name="unmatched_action" value="warn"/>
22856 <param name="aaa_max" value="0"/> 23698 <param name="aaa_max" value="0"/>
22857 <param name="mismatches_max" value="0"/> 23699 <param name="mismatches_max" value="0"/>
22858 <param name="IL_equivalent" value="false"/> 23700 <param name="IL_equivalent" value="false"/>
22859 <section name="enzyme"> 23701 <section name="enzyme">
22860 <param name="name" value="Trypsin"/> 23702 <param name="name" value="auto"/>
22861 <param name="specificity" value="none"/> 23703 <param name="specificity" value="none"/>
22862 </section> 23704 </section>
22863 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22864 <output name="ctd_out" ftype="xml"> 23706 <output name="ctd_out" ftype="xml">
22865 <assert_contents> 23707 <assert_contents>
22880 <param name="decoy_string_position" value="prefix"/> 23722 <param name="decoy_string_position" value="prefix"/>
22881 <param name="missing_decoy_action" value="error"/> 23723 <param name="missing_decoy_action" value="error"/>
22882 <param name="write_protein_sequence" value="false"/> 23724 <param name="write_protein_sequence" value="false"/>
22883 <param name="write_protein_description" value="false"/> 23725 <param name="write_protein_description" value="false"/>
22884 <param name="keep_unreferenced_proteins" value="false"/> 23726 <param name="keep_unreferenced_proteins" value="false"/>
22885 <param name="allow_unmatched" value="true"/> 23727 <param name="unmatched_action" value="warn"/>
22886 <param name="aaa_max" value="4"/> 23728 <param name="aaa_max" value="4"/>
22887 <param name="mismatches_max" value="0"/> 23729 <param name="mismatches_max" value="0"/>
22888 <param name="IL_equivalent" value="false"/> 23730 <param name="IL_equivalent" value="false"/>
22889 <section name="enzyme"> 23731 <section name="enzyme">
22890 <param name="name" value="Trypsin"/> 23732 <param name="name" value="auto"/>
22891 <param name="specificity" value="none"/> 23733 <param name="specificity" value="none"/>
22892 </section> 23734 </section>
22893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23735 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22894 <output name="ctd_out" ftype="xml"> 23736 <output name="ctd_out" ftype="xml">
22895 <assert_contents> 23737 <assert_contents>
22910 <param name="decoy_string_position" value="prefix"/> 23752 <param name="decoy_string_position" value="prefix"/>
22911 <param name="missing_decoy_action" value="error"/> 23753 <param name="missing_decoy_action" value="error"/>
22912 <param name="write_protein_sequence" value="false"/> 23754 <param name="write_protein_sequence" value="false"/>
22913 <param name="write_protein_description" value="false"/> 23755 <param name="write_protein_description" value="false"/>
22914 <param name="keep_unreferenced_proteins" value="false"/> 23756 <param name="keep_unreferenced_proteins" value="false"/>
22915 <param name="allow_unmatched" value="true"/> 23757 <param name="unmatched_action" value="warn"/>
22916 <param name="aaa_max" value="3"/> 23758 <param name="aaa_max" value="3"/>
22917 <param name="mismatches_max" value="0"/> 23759 <param name="mismatches_max" value="0"/>
22918 <param name="IL_equivalent" value="false"/> 23760 <param name="IL_equivalent" value="false"/>
22919 <section name="enzyme"> 23761 <section name="enzyme">
22920 <param name="name" value="Trypsin"/> 23762 <param name="name" value="auto"/>
22921 <param name="specificity" value="none"/> 23763 <param name="specificity" value="none"/>
22922 </section> 23764 </section>
22923 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23765 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22924 <output name="ctd_out" ftype="xml"> 23766 <output name="ctd_out" ftype="xml">
22925 <assert_contents> 23767 <assert_contents>
22940 <param name="decoy_string_position" value="prefix"/> 23782 <param name="decoy_string_position" value="prefix"/>
22941 <param name="missing_decoy_action" value="error"/> 23783 <param name="missing_decoy_action" value="error"/>
22942 <param name="write_protein_sequence" value="false"/> 23784 <param name="write_protein_sequence" value="false"/>
22943 <param name="write_protein_description" value="false"/> 23785 <param name="write_protein_description" value="false"/>
22944 <param name="keep_unreferenced_proteins" value="false"/> 23786 <param name="keep_unreferenced_proteins" value="false"/>
22945 <param name="allow_unmatched" value="true"/> 23787 <param name="unmatched_action" value="warn"/>
22946 <param name="aaa_max" value="4"/> 23788 <param name="aaa_max" value="4"/>
22947 <param name="mismatches_max" value="0"/> 23789 <param name="mismatches_max" value="0"/>
22948 <param name="IL_equivalent" value="false"/> 23790 <param name="IL_equivalent" value="false"/>
22949 <section name="enzyme"> 23791 <section name="enzyme">
22950 <param name="name" value="Trypsin"/> 23792 <param name="name" value="auto"/>
22951 <param name="specificity" value="full"/> 23793 <param name="specificity" value="full"/>
22952 </section> 23794 </section>
22953 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23795 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22954 <output name="ctd_out" ftype="xml"> 23796 <output name="ctd_out" ftype="xml">
22955 <assert_contents> 23797 <assert_contents>
22970 <param name="decoy_string_position" value="prefix"/> 23812 <param name="decoy_string_position" value="prefix"/>
22971 <param name="missing_decoy_action" value="error"/> 23813 <param name="missing_decoy_action" value="error"/>
22972 <param name="write_protein_sequence" value="false"/> 23814 <param name="write_protein_sequence" value="false"/>
22973 <param name="write_protein_description" value="false"/> 23815 <param name="write_protein_description" value="false"/>
22974 <param name="keep_unreferenced_proteins" value="false"/> 23816 <param name="keep_unreferenced_proteins" value="false"/>
22975 <param name="allow_unmatched" value="true"/> 23817 <param name="unmatched_action" value="warn"/>
22976 <param name="aaa_max" value="4"/> 23818 <param name="aaa_max" value="4"/>
22977 <param name="mismatches_max" value="0"/> 23819 <param name="mismatches_max" value="0"/>
22978 <param name="IL_equivalent" value="false"/> 23820 <param name="IL_equivalent" value="false"/>
22979 <section name="enzyme"> 23821 <section name="enzyme">
22980 <param name="name" value="Trypsin"/> 23822 <param name="name" value="auto"/>
22981 <param name="specificity" value="semi"/> 23823 <param name="specificity" value="semi"/>
22982 </section> 23824 </section>
22983 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22984 <output name="ctd_out" ftype="xml"> 23826 <output name="ctd_out" ftype="xml">
22985 <assert_contents> 23827 <assert_contents>
23000 <param name="decoy_string_position" value="prefix"/> 23842 <param name="decoy_string_position" value="prefix"/>
23001 <param name="missing_decoy_action" value="error"/> 23843 <param name="missing_decoy_action" value="error"/>
23002 <param name="write_protein_sequence" value="false"/> 23844 <param name="write_protein_sequence" value="false"/>
23003 <param name="write_protein_description" value="false"/> 23845 <param name="write_protein_description" value="false"/>
23004 <param name="keep_unreferenced_proteins" value="false"/> 23846 <param name="keep_unreferenced_proteins" value="false"/>
23005 <param name="allow_unmatched" value="true"/> 23847 <param name="unmatched_action" value="remove"/>
23006 <param name="aaa_max" value="4"/> 23848 <param name="aaa_max" value="4"/>
23007 <param name="mismatches_max" value="0"/> 23849 <param name="mismatches_max" value="0"/>
23008 <param name="IL_equivalent" value="false"/> 23850 <param name="IL_equivalent" value="false"/>
23009 <section name="enzyme"> 23851 <section name="enzyme">
23010 <param name="name" value="Trypsin"/> 23852 <param name="name" value="auto"/>
23011 <param name="specificity" value="none"/> 23853 <param name="specificity" value="none"/>
23012 </section> 23854 </section>
23013 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23855 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23014 <output name="ctd_out" ftype="xml"> 23856 <output name="ctd_out" ftype="xml">
23015 <assert_contents> 23857 <assert_contents>
23030 <param name="decoy_string_position" value="prefix"/> 23872 <param name="decoy_string_position" value="prefix"/>
23031 <param name="missing_decoy_action" value="error"/> 23873 <param name="missing_decoy_action" value="error"/>
23032 <param name="write_protein_sequence" value="true"/> 23874 <param name="write_protein_sequence" value="true"/>
23033 <param name="write_protein_description" value="false"/> 23875 <param name="write_protein_description" value="false"/>
23034 <param name="keep_unreferenced_proteins" value="false"/> 23876 <param name="keep_unreferenced_proteins" value="false"/>
23035 <param name="allow_unmatched" value="false"/> 23877 <param name="unmatched_action" value="error"/>
23036 <param name="aaa_max" value="3"/> 23878 <param name="aaa_max" value="3"/>
23037 <param name="mismatches_max" value="0"/> 23879 <param name="mismatches_max" value="0"/>
23038 <param name="IL_equivalent" value="true"/> 23880 <param name="IL_equivalent" value="true"/>
23039 <section name="enzyme"> 23881 <section name="enzyme">
23040 <param name="name" value="Trypsin"/> 23882 <param name="name" value="auto"/>
23041 <param name="specificity" value="full"/> 23883 <param name="specificity" value="auto"/>
23042 </section> 23884 </section>
23043 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23885 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23044 <output name="ctd_out" ftype="xml"> 23886 <output name="ctd_out" ftype="xml">
23045 <assert_contents> 23887 <assert_contents>
23046 <is_valid_xml/> 23888 <is_valid_xml/>
23060 <param name="decoy_string_position" value="prefix"/> 23902 <param name="decoy_string_position" value="prefix"/>
23061 <param name="missing_decoy_action" value="error"/> 23903 <param name="missing_decoy_action" value="error"/>
23062 <param name="write_protein_sequence" value="false"/> 23904 <param name="write_protein_sequence" value="false"/>
23063 <param name="write_protein_description" value="false"/> 23905 <param name="write_protein_description" value="false"/>
23064 <param name="keep_unreferenced_proteins" value="false"/> 23906 <param name="keep_unreferenced_proteins" value="false"/>
23065 <param name="allow_unmatched" value="true"/> 23907 <param name="unmatched_action" value="warn"/>
23066 <param name="aaa_max" value="4"/> 23908 <param name="aaa_max" value="4"/>
23067 <param name="mismatches_max" value="0"/> 23909 <param name="mismatches_max" value="0"/>
23068 <param name="IL_equivalent" value="false"/> 23910 <param name="IL_equivalent" value="false"/>
23069 <section name="enzyme"> 23911 <section name="enzyme">
23070 <param name="name" value="Trypsin"/> 23912 <param name="name" value="auto"/>
23071 <param name="specificity" value="none"/> 23913 <param name="specificity" value="none"/>
23072 </section> 23914 </section>
23073 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23915 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23074 <output name="ctd_out" ftype="xml"> 23916 <output name="ctd_out" ftype="xml">
23075 <assert_contents> 23917 <assert_contents>
23090 <param name="decoy_string_position" value="prefix"/> 23932 <param name="decoy_string_position" value="prefix"/>
23091 <param name="missing_decoy_action" value="error"/> 23933 <param name="missing_decoy_action" value="error"/>
23092 <param name="write_protein_sequence" value="false"/> 23934 <param name="write_protein_sequence" value="false"/>
23093 <param name="write_protein_description" value="false"/> 23935 <param name="write_protein_description" value="false"/>
23094 <param name="keep_unreferenced_proteins" value="false"/> 23936 <param name="keep_unreferenced_proteins" value="false"/>
23095 <param name="allow_unmatched" value="false"/> 23937 <param name="unmatched_action" value="error"/>
23096 <param name="aaa_max" value="4"/> 23938 <param name="aaa_max" value="4"/>
23097 <param name="mismatches_max" value="0"/> 23939 <param name="mismatches_max" value="0"/>
23098 <param name="IL_equivalent" value="false"/> 23940 <param name="IL_equivalent" value="false"/>
23099 <section name="enzyme"> 23941 <section name="enzyme">
23100 <param name="name" value="Trypsin"/> 23942 <param name="name" value="auto"/>
23101 <param name="specificity" value="full"/> 23943 <param name="specificity" value="auto"/>
23102 </section> 23944 </section>
23103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23945 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23104 <output name="ctd_out" ftype="xml"> 23946 <output name="ctd_out" ftype="xml">
23105 <assert_contents> 23947 <assert_contents>
23106 <is_valid_xml/> 23948 <is_valid_xml/>
23120 <param name="decoy_string_position" value="prefix"/> 23962 <param name="decoy_string_position" value="prefix"/>
23121 <param name="missing_decoy_action" value="error"/> 23963 <param name="missing_decoy_action" value="error"/>
23122 <param name="write_protein_sequence" value="true"/> 23964 <param name="write_protein_sequence" value="true"/>
23123 <param name="write_protein_description" value="false"/> 23965 <param name="write_protein_description" value="false"/>
23124 <param name="keep_unreferenced_proteins" value="false"/> 23966 <param name="keep_unreferenced_proteins" value="false"/>
23125 <param name="allow_unmatched" value="false"/> 23967 <param name="unmatched_action" value="error"/>
23126 <param name="aaa_max" value="4"/> 23968 <param name="aaa_max" value="4"/>
23127 <param name="mismatches_max" value="0"/> 23969 <param name="mismatches_max" value="0"/>
23128 <param name="IL_equivalent" value="false"/> 23970 <param name="IL_equivalent" value="false"/>
23129 <section name="enzyme"> 23971 <section name="enzyme">
23130 <param name="name" value="Trypsin"/> 23972 <param name="name" value="auto"/>
23131 <param name="specificity" value="none"/> 23973 <param name="specificity" value="none"/>
23132 </section> 23974 </section>
23133 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 23975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23134 <output name="ctd_out" ftype="xml"> 23976 <output name="ctd_out" ftype="xml">
23135 <assert_contents> 23977 <assert_contents>
23147 <param name="cpos" value="0.0"/> 23989 <param name="cpos" value="0.0"/>
23148 <param name="cneg" value="0.0"/> 23990 <param name="cneg" value="0.0"/>
23149 <param name="testFDR" value="0.5"/> 23991 <param name="testFDR" value="0.5"/>
23150 <param name="trainFDR" value="0.5"/> 23992 <param name="trainFDR" value="0.5"/>
23151 <param name="maxiter" value="10"/> 23993 <param name="maxiter" value="10"/>
23994 <param name="nested_xval_bins" value="1"/>
23152 <param name="quick_validation" value="false"/> 23995 <param name="quick_validation" value="false"/>
23996 <param name="static" value="false"/>
23153 <param name="default_direction" value=""/> 23997 <param name="default_direction" value=""/>
23154 <param name="verbose" value="2"/> 23998 <param name="verbose" value="2"/>
23155 <param name="unitnorm" value="false"/> 23999 <param name="unitnorm" value="false"/>
23156 <param name="test_each_iteration" value="false"/> 24000 <param name="test_each_iteration" value="false"/>
23157 <param name="override" value="false"/> 24001 <param name="override" value="false"/>
23190 <param name="cpos" value="0.0"/> 24034 <param name="cpos" value="0.0"/>
23191 <param name="cneg" value="0.0"/> 24035 <param name="cneg" value="0.0"/>
23192 <param name="testFDR" value="0.01"/> 24036 <param name="testFDR" value="0.01"/>
23193 <param name="trainFDR" value="0.01"/> 24037 <param name="trainFDR" value="0.01"/>
23194 <param name="maxiter" value="10"/> 24038 <param name="maxiter" value="10"/>
24039 <param name="nested_xval_bins" value="1"/>
23195 <param name="quick_validation" value="false"/> 24040 <param name="quick_validation" value="false"/>
24041 <param name="static" value="false"/>
23196 <param name="default_direction" value=""/> 24042 <param name="default_direction" value=""/>
23197 <param name="verbose" value="2"/> 24043 <param name="verbose" value="2"/>
23198 <param name="unitnorm" value="false"/> 24044 <param name="unitnorm" value="false"/>
23199 <param name="test_each_iteration" value="false"/> 24045 <param name="test_each_iteration" value="false"/>
23200 <param name="override" value="false"/> 24046 <param name="override" value="false"/>
23233 <param name="cpos" value="0.0"/> 24079 <param name="cpos" value="0.0"/>
23234 <param name="cneg" value="0.0"/> 24080 <param name="cneg" value="0.0"/>
23235 <param name="testFDR" value="0.01"/> 24081 <param name="testFDR" value="0.01"/>
23236 <param name="trainFDR" value="0.01"/> 24082 <param name="trainFDR" value="0.01"/>
23237 <param name="maxiter" value="10"/> 24083 <param name="maxiter" value="10"/>
24084 <param name="nested_xval_bins" value="1"/>
23238 <param name="quick_validation" value="false"/> 24085 <param name="quick_validation" value="false"/>
24086 <param name="static" value="false"/>
23239 <param name="default_direction" value=""/> 24087 <param name="default_direction" value=""/>
23240 <param name="verbose" value="2"/> 24088 <param name="verbose" value="2"/>
23241 <param name="unitnorm" value="false"/> 24089 <param name="unitnorm" value="false"/>
23242 <param name="test_each_iteration" value="false"/> 24090 <param name="test_each_iteration" value="false"/>
23243 <param name="override" value="false"/> 24091 <param name="override" value="false"/>
23276 <param name="cpos" value="0.0"/> 24124 <param name="cpos" value="0.0"/>
23277 <param name="cneg" value="0.0"/> 24125 <param name="cneg" value="0.0"/>
23278 <param name="testFDR" value="0.01"/> 24126 <param name="testFDR" value="0.01"/>
23279 <param name="trainFDR" value="0.01"/> 24127 <param name="trainFDR" value="0.01"/>
23280 <param name="maxiter" value="10"/> 24128 <param name="maxiter" value="10"/>
24129 <param name="nested_xval_bins" value="1"/>
23281 <param name="quick_validation" value="false"/> 24130 <param name="quick_validation" value="false"/>
24131 <param name="static" value="false"/>
23282 <param name="default_direction" value=""/> 24132 <param name="default_direction" value=""/>
23283 <param name="verbose" value="2"/> 24133 <param name="verbose" value="2"/>
23284 <param name="unitnorm" value="false"/> 24134 <param name="unitnorm" value="false"/>
23285 <param name="test_each_iteration" value="false"/> 24135 <param name="test_each_iteration" value="false"/>
23286 <param name="override" value="false"/> 24136 <param name="override" value="false"/>
23319 <param name="cpos" value="0.0"/> 24169 <param name="cpos" value="0.0"/>
23320 <param name="cneg" value="0.0"/> 24170 <param name="cneg" value="0.0"/>
23321 <param name="testFDR" value="0.5"/> 24171 <param name="testFDR" value="0.5"/>
23322 <param name="trainFDR" value="0.5"/> 24172 <param name="trainFDR" value="0.5"/>
23323 <param name="maxiter" value="10"/> 24173 <param name="maxiter" value="10"/>
24174 <param name="nested_xval_bins" value="1"/>
23324 <param name="quick_validation" value="false"/> 24175 <param name="quick_validation" value="false"/>
24176 <param name="static" value="false"/>
23325 <param name="default_direction" value=""/> 24177 <param name="default_direction" value=""/>
23326 <param name="verbose" value="2"/> 24178 <param name="verbose" value="2"/>
23327 <param name="unitnorm" value="false"/> 24179 <param name="unitnorm" value="false"/>
23328 <param name="test_each_iteration" value="false"/> 24180 <param name="test_each_iteration" value="false"/>
23329 <param name="override" value="false"/> 24181 <param name="override" value="false"/>
23537 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 24389 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23538 <param name="merge_runs" value="all"/> 24390 <param name="merge_runs" value="all"/>
23539 <param name="annotate_indist_groups" value="true"/> 24391 <param name="annotate_indist_groups" value="true"/>
23540 <section name="Merging"> 24392 <section name="Merging">
23541 <param name="annotate_origin" value="false"/> 24393 <param name="annotate_origin" value="false"/>
24394 <param name="allow_disagreeing_settings" value="false"/>
23542 </section> 24395 </section>
23543 <section name="Algorithm"> 24396 <section name="Algorithm">
23544 <param name="min_peptides_per_protein" value="1"/> 24397 <param name="min_peptides_per_protein" value="1"/>
23545 <param name="score_aggregation_method" value="maximum"/> 24398 <param name="score_aggregation_method" value="maximum"/>
23546 <param name="treat_charge_variants_separately" value="true"/> 24399 <param name="treat_charge_variants_separately" value="true"/>
23806 <assert_contents> 24659 <assert_contents>
23807 <is_valid_xml/> 24660 <is_valid_xml/>
23808 </assert_contents> 24661 </assert_contents>
23809 </output> 24662 </output>
23810 </test> 24663 </test>
23811 <test expect_num_outputs="2"> 24664 <test expect_num_outputs="3">
23812 <conditional name="adv_opts_cond"> 24665 <conditional name="adv_opts_cond">
23813 <param name="adv_opts_selector" value="advanced"/> 24666 <param name="adv_opts_selector" value="advanced"/>
23814 <param name="force" value="false"/> 24667 <param name="force" value="false"/>
23815 <param name="test" value="true"/> 24668 <param name="test" value="true"/>
23816 </conditional> 24669 </conditional>
23817 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 24670 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23818 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 24671 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
24672 <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
23819 <param name="top" value="3"/> 24673 <param name="top" value="3"/>
23820 <param name="average" value="sum"/> 24674 <param name="average" value="sum"/>
23821 <param name="include_all" value="true"/> 24675 <param name="include_all" value="true"/>
23822 <param name="best_charge_and_fraction" value="false"/> 24676 <param name="best_charge_and_fraction" value="false"/>
23823 <param name="greedy_group_resolution" value="false"/> 24677 <param name="greedy_group_resolution" value="false"/>
23830 <section name="format"> 24684 <section name="format">
23831 <param name="separator" value=""/> 24685 <param name="separator" value=""/>
23832 <param name="quoting" value="double"/> 24686 <param name="quoting" value="double"/>
23833 <param name="replacement" value="_"/> 24687 <param name="replacement" value="_"/>
23834 </section> 24688 </section>
23835 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 24689 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
23836 <output name="ctd_out" ftype="xml"> 24690 <output name="ctd_out" ftype="xml">
23837 <assert_contents> 24691 <assert_contents>
23838 <is_valid_xml/> 24692 <is_valid_xml/>
23839 </assert_contents> 24693 </assert_contents>
23840 </output> 24694 </output>
24045 <section name="FragmentMassError"> 24899 <section name="FragmentMassError">
24046 <param name="unit" value="auto"/> 24900 <param name="unit" value="auto"/>
24047 <param name="tolerance" value="20.0"/> 24901 <param name="tolerance" value="20.0"/>
24048 </section> 24902 </section>
24049 <section name="MS2_id_rate"> 24903 <section name="MS2_id_rate">
24050 <param name="force_no_fdr" value="false"/> 24904 <param name="assume_all_target" value="false"/>
24051 </section> 24905 </section>
24052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/> 24906 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
24053 <output name="ctd_out" ftype="xml"> 24907 <output name="ctd_out" ftype="xml">
24054 <assert_contents> 24908 <assert_contents>
24055 <is_valid_xml/> 24909 <is_valid_xml/>
24056 </assert_contents> 24910 </assert_contents>
24057 </output> 24911 </output>
24568 <param name="in" value="SimpleSearchEngine_1.mzML"/> 25422 <param name="in" value="SimpleSearchEngine_1.mzML"/>
24569 <param name="database" value="SimpleSearchEngine_1.fasta"/> 25423 <param name="database" value="SimpleSearchEngine_1.fasta"/>
24570 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> 25424 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24571 <section name="Search"> 25425 <section name="Search">
24572 <param name="enzyme" value="Trypsin"/> 25426 <param name="enzyme" value="Trypsin"/>
25427 <param name="decoys" value="false"/>
24573 <section name="precursor"> 25428 <section name="precursor">
24574 <param name="mass_tolerance" value="5.0"/> 25429 <param name="mass_tolerance" value="5.0"/>
24575 <param name="mass_tolerance_unit" value="ppm"/> 25430 <param name="mass_tolerance_unit" value="ppm"/>
24576 <param name="min_charge" value="2"/> 25431 <param name="min_charge" value="2"/>
24577 <param name="max_charge" value="5"/> 25432 <param name="max_charge" value="5"/>
24583 </section> 25438 </section>
24584 <section name="modifications"> 25439 <section name="modifications">
24585 <param name="fixed" value=""/> 25440 <param name="fixed" value=""/>
24586 <param name="variable" value="Oxidation (M)"/> 25441 <param name="variable" value="Oxidation (M)"/>
24587 <param name="variable_max_per_peptide" value="2"/> 25442 <param name="variable_max_per_peptide" value="2"/>
25443 </section>
25444 <section name="annotate">
25445 <param name="PSM" value=""/>
24588 </section> 25446 </section>
24589 <section name="peptide"> 25447 <section name="peptide">
24590 <param name="min_size" value="7"/> 25448 <param name="min_size" value="7"/>
24591 <param name="max_size" value="40"/> 25449 <param name="max_size" value="40"/>
24592 <param name="missed_cleavages" value="1"/> 25450 <param name="missed_cleavages" value="1"/>
24633 <param name="isotope" value="both"/> 25491 <param name="isotope" value="both"/>
24634 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25492 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24635 <param name="compound_timeout" value="10"/> 25493 <param name="compound_timeout" value="10"/>
24636 <param name="tree_timeout" value="0"/> 25494 <param name="tree_timeout" value="0"/>
24637 <param name="top_n_hits" value="10"/> 25495 <param name="top_n_hits" value="10"/>
24638 <param name="cores" value="1"/>
24639 <param name="auto_charge" value="true"/> 25496 <param name="auto_charge" value="true"/>
24640 <param name="ion_tree" value="false"/> 25497 <param name="ion_tree" value="false"/>
24641 <param name="no_recalibration" value="false"/> 25498 <param name="no_recalibration" value="false"/>
24642 <param name="most_intense_ms2" value="false"/> 25499 <param name="most_intense_ms2" value="false"/>
24643 </section> 25500 </section>
24677 <param name="isotope" value="both"/> 25534 <param name="isotope" value="both"/>
24678 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25535 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24679 <param name="compound_timeout" value="10"/> 25536 <param name="compound_timeout" value="10"/>
24680 <param name="tree_timeout" value="0"/> 25537 <param name="tree_timeout" value="0"/>
24681 <param name="top_n_hits" value="10"/> 25538 <param name="top_n_hits" value="10"/>
24682 <param name="cores" value="1"/>
24683 <param name="auto_charge" value="true"/> 25539 <param name="auto_charge" value="true"/>
24684 <param name="ion_tree" value="false"/> 25540 <param name="ion_tree" value="false"/>
24685 <param name="no_recalibration" value="false"/> 25541 <param name="no_recalibration" value="false"/>
24686 <param name="most_intense_ms2" value="false"/> 25542 <param name="most_intense_ms2" value="false"/>
24687 </section> 25543 </section>
24721 <param name="isotope" value="both"/> 25577 <param name="isotope" value="both"/>
24722 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25578 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24723 <param name="compound_timeout" value="10"/> 25579 <param name="compound_timeout" value="10"/>
24724 <param name="tree_timeout" value="0"/> 25580 <param name="tree_timeout" value="0"/>
24725 <param name="top_n_hits" value="10"/> 25581 <param name="top_n_hits" value="10"/>
24726 <param name="cores" value="1"/>
24727 <param name="auto_charge" value="true"/> 25582 <param name="auto_charge" value="true"/>
24728 <param name="ion_tree" value="false"/> 25583 <param name="ion_tree" value="false"/>
24729 <param name="no_recalibration" value="false"/> 25584 <param name="no_recalibration" value="false"/>
24730 <param name="most_intense_ms2" value="false"/> 25585 <param name="most_intense_ms2" value="false"/>
24731 </section> 25586 </section>
24765 <param name="isotope" value="both"/> 25620 <param name="isotope" value="both"/>
24766 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25621 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24767 <param name="compound_timeout" value="10"/> 25622 <param name="compound_timeout" value="10"/>
24768 <param name="tree_timeout" value="0"/> 25623 <param name="tree_timeout" value="0"/>
24769 <param name="top_n_hits" value="10"/> 25624 <param name="top_n_hits" value="10"/>
24770 <param name="cores" value="1"/>
24771 <param name="auto_charge" value="false"/> 25625 <param name="auto_charge" value="false"/>
24772 <param name="ion_tree" value="false"/> 25626 <param name="ion_tree" value="false"/>
24773 <param name="no_recalibration" value="false"/> 25627 <param name="no_recalibration" value="false"/>
24774 <param name="most_intense_ms2" value="false"/> 25628 <param name="most_intense_ms2" value="false"/>
24775 </section> 25629 </section>
24809 <param name="isotope" value="both"/> 25663 <param name="isotope" value="both"/>
24810 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25664 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24811 <param name="compound_timeout" value="10"/> 25665 <param name="compound_timeout" value="10"/>
24812 <param name="tree_timeout" value="0"/> 25666 <param name="tree_timeout" value="0"/>
24813 <param name="top_n_hits" value="10"/> 25667 <param name="top_n_hits" value="10"/>
24814 <param name="cores" value="1"/>
24815 <param name="auto_charge" value="false"/> 25668 <param name="auto_charge" value="false"/>
24816 <param name="ion_tree" value="false"/> 25669 <param name="ion_tree" value="false"/>
24817 <param name="no_recalibration" value="false"/> 25670 <param name="no_recalibration" value="false"/>
24818 <param name="most_intense_ms2" value="false"/> 25671 <param name="most_intense_ms2" value="false"/>
24819 </section> 25672 </section>
24853 <param name="isotope" value="both"/> 25706 <param name="isotope" value="both"/>
24854 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25707 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24855 <param name="compound_timeout" value="10"/> 25708 <param name="compound_timeout" value="10"/>
24856 <param name="tree_timeout" value="0"/> 25709 <param name="tree_timeout" value="0"/>
24857 <param name="top_n_hits" value="10"/> 25710 <param name="top_n_hits" value="10"/>
24858 <param name="cores" value="1"/>
24859 <param name="auto_charge" value="false"/> 25711 <param name="auto_charge" value="false"/>
24860 <param name="ion_tree" value="false"/> 25712 <param name="ion_tree" value="false"/>
24861 <param name="no_recalibration" value="false"/> 25713 <param name="no_recalibration" value="false"/>
24862 <param name="most_intense_ms2" value="false"/> 25714 <param name="most_intense_ms2" value="false"/>
24863 </section> 25715 </section>
24890 <param name="no_masstrace_info_isotope_pattern" value="false"/> 25742 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24891 </section> 25743 </section>
24892 <section name="sirius"> 25744 <section name="sirius">
24893 <param name="profile" value="qtof"/> 25745 <param name="profile" value="qtof"/>
24894 <param name="candidates" value="5"/> 25746 <param name="candidates" value="5"/>
24895 <param name="database" value="all"/> 25747 <param name="database" value="pubchem"/>
24896 <param name="noise" value="0"/> 25748 <param name="noise" value="0"/>
24897 <param name="ppm_max" value="10"/> 25749 <param name="ppm_max" value="10"/>
24898 <param name="isotope" value="both"/> 25750 <param name="isotope" value="both"/>
24899 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> 25751 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24900 <param name="compound_timeout" value="10"/> 25752 <param name="compound_timeout" value="10"/>
24901 <param name="tree_timeout" value="0"/> 25753 <param name="tree_timeout" value="0"/>
24902 <param name="top_n_hits" value="10"/> 25754 <param name="top_n_hits" value="10"/>
24903 <param name="cores" value="1"/>
24904 <param name="auto_charge" value="true"/> 25755 <param name="auto_charge" value="true"/>
24905 <param name="ion_tree" value="false"/> 25756 <param name="ion_tree" value="false"/>
24906 <param name="no_recalibration" value="false"/> 25757 <param name="no_recalibration" value="false"/>
24907 <param name="most_intense_ms2" value="false"/> 25758 <param name="most_intense_ms2" value="false"/>
24908 </section> 25759 </section>
25033 </test> 25884 </test>
25034 </xml> 25885 </xml>
25035 <xml name="autotest_SpectraMerger"> 25886 <xml name="autotest_SpectraMerger">
25036 </xml> 25887 </xml>
25037 <xml name="autotest_SpectraSTSearchAdapter"/> 25888 <xml name="autotest_SpectraSTSearchAdapter"/>
25889 <xml name="autotest_StaticModification">
25890 </xml>
25038 <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> 25891 <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
25039 </xml> 25892 </xml>
25040 <xml name="autotest_TargetedFileConverter"> 25893 <xml name="autotest_TargetedFileConverter">
25041 <test expect_num_outputs="2"> 25894 <test expect_num_outputs="2">
25042 <conditional name="adv_opts_cond"> 25895 <conditional name="adv_opts_cond">
25485 <param name="adv_opts_selector" value="advanced"/> 26338 <param name="adv_opts_selector" value="advanced"/>
25486 <param name="force" value="false"/> 26339 <param name="force" value="false"/>
25487 <param name="test" value="true"/> 26340 <param name="test" value="true"/>
25488 </conditional> 26341 </conditional>
25489 <param name="in" value="TextExporter_1_input.featureXML"/> 26342 <param name="in" value="TextExporter_1_input.featureXML"/>
25490 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 26343 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25491 <param name="separator" value=""/> 26344 <param name="separator" value=""/>
25492 <param name="replacement" value="_"/> 26345 <param name="replacement" value="_"/>
25493 <param name="quoting" value="none"/> 26346 <param name="quoting" value="none"/>
25494 <param name="no_ids" value="false"/> 26347 <param name="no_ids" value="false"/>
25495 <section name="feature"> 26348 <section name="feature">
25508 <section name="consensus"> 26361 <section name="consensus">
25509 <param name="sorting_method" value="none"/> 26362 <param name="sorting_method" value="none"/>
25510 <param name="sort_by_maps" value="false"/> 26363 <param name="sort_by_maps" value="false"/>
25511 <param name="sort_by_size" value="false"/> 26364 <param name="sort_by_size" value="false"/>
25512 </section> 26365 </section>
25513 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26366 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25514 <output name="ctd_out" ftype="xml"> 26367 <output name="ctd_out" ftype="xml">
25515 <assert_contents> 26368 <assert_contents>
25516 <is_valid_xml/> 26369 <is_valid_xml/>
25517 </assert_contents> 26370 </assert_contents>
25518 </output> 26371 </output>
25522 <param name="adv_opts_selector" value="advanced"/> 26375 <param name="adv_opts_selector" value="advanced"/>
25523 <param name="force" value="false"/> 26376 <param name="force" value="false"/>
25524 <param name="test" value="true"/> 26377 <param name="test" value="true"/>
25525 </conditional> 26378 </conditional>
25526 <param name="in" value="TextExporter_2_input.consensusXML"/> 26379 <param name="in" value="TextExporter_2_input.consensusXML"/>
25527 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/> 26380 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
25528 <param name="separator" value=""/> 26381 <param name="separator" value=""/>
25529 <param name="replacement" value="_"/> 26382 <param name="replacement" value="_"/>
25530 <param name="quoting" value="none"/> 26383 <param name="quoting" value="none"/>
25531 <param name="no_ids" value="true"/> 26384 <param name="no_ids" value="true"/>
25532 <section name="feature"> 26385 <section name="feature">
25548 <param name="sort_by_size" value="true"/> 26401 <param name="sort_by_size" value="true"/>
25549 </section> 26402 </section>
25550 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> 26403 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25551 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> 26404 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25552 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> 26405 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25553 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> 26406 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
25554 <output name="ctd_out" ftype="xml"> 26407 <output name="ctd_out" ftype="xml">
25555 <assert_contents> 26408 <assert_contents>
25556 <is_valid_xml/> 26409 <is_valid_xml/>
25557 </assert_contents> 26410 </assert_contents>
25558 </output> 26411 </output>
25562 <param name="adv_opts_selector" value="advanced"/> 26415 <param name="adv_opts_selector" value="advanced"/>
25563 <param name="force" value="false"/> 26416 <param name="force" value="false"/>
25564 <param name="test" value="true"/> 26417 <param name="test" value="true"/>
25565 </conditional> 26418 </conditional>
25566 <param name="in" value="TextExporter_3_input.idXML"/> 26419 <param name="in" value="TextExporter_3_input.idXML"/>
25567 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 26420 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25568 <param name="separator" value=""/> 26421 <param name="separator" value=""/>
25569 <param name="replacement" value="_"/> 26422 <param name="replacement" value="_"/>
25570 <param name="quoting" value="none"/> 26423 <param name="quoting" value="none"/>
25571 <param name="no_ids" value="false"/> 26424 <param name="no_ids" value="false"/>
25572 <section name="feature"> 26425 <section name="feature">
25585 <section name="consensus"> 26438 <section name="consensus">
25586 <param name="sorting_method" value="none"/> 26439 <param name="sorting_method" value="none"/>
25587 <param name="sort_by_maps" value="false"/> 26440 <param name="sort_by_maps" value="false"/>
25588 <param name="sort_by_size" value="false"/> 26441 <param name="sort_by_size" value="false"/>
25589 </section> 26442 </section>
25590 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26443 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25591 <output name="ctd_out" ftype="xml"> 26444 <output name="ctd_out" ftype="xml">
25592 <assert_contents> 26445 <assert_contents>
25593 <is_valid_xml/> 26446 <is_valid_xml/>
25594 </assert_contents> 26447 </assert_contents>
25595 </output> 26448 </output>
25599 <param name="adv_opts_selector" value="advanced"/> 26452 <param name="adv_opts_selector" value="advanced"/>
25600 <param name="force" value="false"/> 26453 <param name="force" value="false"/>
25601 <param name="test" value="true"/> 26454 <param name="test" value="true"/>
25602 </conditional> 26455 </conditional>
25603 <param name="in" value="TextExporter_3_input.idXML"/> 26456 <param name="in" value="TextExporter_3_input.idXML"/>
25604 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/> 26457 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25605 <param name="separator" value=""/> 26458 <param name="separator" value=""/>
25606 <param name="replacement" value="_"/> 26459 <param name="replacement" value="_"/>
25607 <param name="quoting" value="none"/> 26460 <param name="quoting" value="none"/>
25608 <param name="no_ids" value="false"/> 26461 <param name="no_ids" value="false"/>
25609 <section name="feature"> 26462 <section name="feature">
25622 <section name="consensus"> 26475 <section name="consensus">
25623 <param name="sorting_method" value="none"/> 26476 <param name="sorting_method" value="none"/>
25624 <param name="sort_by_maps" value="false"/> 26477 <param name="sort_by_maps" value="false"/>
25625 <param name="sort_by_size" value="false"/> 26478 <param name="sort_by_size" value="false"/>
25626 </section> 26479 </section>
25627 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26480 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25628 <output name="ctd_out" ftype="xml"> 26481 <output name="ctd_out" ftype="xml">
25629 <assert_contents> 26482 <assert_contents>
25630 <is_valid_xml/> 26483 <is_valid_xml/>
25631 </assert_contents> 26484 </assert_contents>
25632 </output> 26485 </output>
25636 <param name="adv_opts_selector" value="advanced"/> 26489 <param name="adv_opts_selector" value="advanced"/>
25637 <param name="force" value="false"/> 26490 <param name="force" value="false"/>
25638 <param name="test" value="true"/> 26491 <param name="test" value="true"/>
25639 </conditional> 26492 </conditional>
25640 <param name="in" value="TextExporter_5_input.idXML"/> 26493 <param name="in" value="TextExporter_5_input.idXML"/>
25641 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/> 26494 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25642 <param name="separator" value=""/> 26495 <param name="separator" value=""/>
25643 <param name="replacement" value="_"/> 26496 <param name="replacement" value="_"/>
25644 <param name="quoting" value="none"/> 26497 <param name="quoting" value="none"/>
25645 <param name="no_ids" value="false"/> 26498 <param name="no_ids" value="false"/>
25646 <section name="feature"> 26499 <section name="feature">
25659 <section name="consensus"> 26512 <section name="consensus">
25660 <param name="sorting_method" value="none"/> 26513 <param name="sorting_method" value="none"/>
25661 <param name="sort_by_maps" value="false"/> 26514 <param name="sort_by_maps" value="false"/>
25662 <param name="sort_by_size" value="false"/> 26515 <param name="sort_by_size" value="false"/>
25663 </section> 26516 </section>
25664 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26517 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25665 <output name="ctd_out" ftype="xml"> 26518 <output name="ctd_out" ftype="xml">
25666 <assert_contents> 26519 <assert_contents>
25667 <is_valid_xml/> 26520 <is_valid_xml/>
25668 </assert_contents> 26521 </assert_contents>
25669 </output> 26522 </output>
25673 <param name="adv_opts_selector" value="advanced"/> 26526 <param name="adv_opts_selector" value="advanced"/>
25674 <param name="force" value="false"/> 26527 <param name="force" value="false"/>
25675 <param name="test" value="true"/> 26528 <param name="test" value="true"/>
25676 </conditional> 26529 </conditional>
25677 <param name="in" value="TextExporter_6_input.featureXML"/> 26530 <param name="in" value="TextExporter_6_input.featureXML"/>
25678 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 26531 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25679 <param name="separator" value=""/> 26532 <param name="separator" value=""/>
25680 <param name="replacement" value="_"/> 26533 <param name="replacement" value="_"/>
25681 <param name="quoting" value="none"/> 26534 <param name="quoting" value="none"/>
25682 <param name="no_ids" value="true"/> 26535 <param name="no_ids" value="true"/>
25683 <section name="feature"> 26536 <section name="feature">
25696 <section name="consensus"> 26549 <section name="consensus">
25697 <param name="sorting_method" value="none"/> 26550 <param name="sorting_method" value="none"/>
25698 <param name="sort_by_maps" value="false"/> 26551 <param name="sort_by_maps" value="false"/>
25699 <param name="sort_by_size" value="false"/> 26552 <param name="sort_by_size" value="false"/>
25700 </section> 26553 </section>
25701 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25702 <output name="ctd_out" ftype="xml"> 26555 <output name="ctd_out" ftype="xml">
25703 <assert_contents> 26556 <assert_contents>
25704 <is_valid_xml/> 26557 <is_valid_xml/>
25705 </assert_contents> 26558 </assert_contents>
25706 </output> 26559 </output>
25710 <param name="adv_opts_selector" value="advanced"/> 26563 <param name="adv_opts_selector" value="advanced"/>
25711 <param name="force" value="false"/> 26564 <param name="force" value="false"/>
25712 <param name="test" value="true"/> 26565 <param name="test" value="true"/>
25713 </conditional> 26566 </conditional>
25714 <param name="in" value="TextExporter_7_input.consensusXML"/> 26567 <param name="in" value="TextExporter_7_input.consensusXML"/>
25715 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/> 26568 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
25716 <param name="separator" value=""/> 26569 <param name="separator" value=""/>
25717 <param name="replacement" value="_"/> 26570 <param name="replacement" value="_"/>
25718 <param name="quoting" value="none"/> 26571 <param name="quoting" value="none"/>
25719 <param name="no_ids" value="false"/> 26572 <param name="no_ids" value="false"/>
25720 <section name="feature"> 26573 <section name="feature">
25733 <section name="consensus"> 26586 <section name="consensus">
25734 <param name="sorting_method" value="RT_then_MZ"/> 26587 <param name="sorting_method" value="RT_then_MZ"/>
25735 <param name="sort_by_maps" value="true"/> 26588 <param name="sort_by_maps" value="true"/>
25736 <param name="sort_by_size" value="true"/> 26589 <param name="sort_by_size" value="true"/>
25737 </section> 26590 </section>
25738 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26591 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25739 <output name="ctd_out" ftype="xml"> 26592 <output name="ctd_out" ftype="xml">
25740 <assert_contents> 26593 <assert_contents>
25741 <is_valid_xml/> 26594 <is_valid_xml/>
25742 </assert_contents> 26595 </assert_contents>
25743 </output> 26596 </output>
25747 <param name="adv_opts_selector" value="advanced"/> 26600 <param name="adv_opts_selector" value="advanced"/>
25748 <param name="force" value="false"/> 26601 <param name="force" value="false"/>
25749 <param name="test" value="true"/> 26602 <param name="test" value="true"/>
25750 </conditional> 26603 </conditional>
25751 <param name="in" value="TextExporter_1_input.featureXML"/> 26604 <param name="in" value="TextExporter_1_input.featureXML"/>
25752 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 26605 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25753 <param name="separator" value=""/> 26606 <param name="separator" value=""/>
25754 <param name="replacement" value="_"/> 26607 <param name="replacement" value="_"/>
25755 <param name="quoting" value="none"/> 26608 <param name="quoting" value="none"/>
25756 <param name="no_ids" value="true"/> 26609 <param name="no_ids" value="true"/>
25757 <section name="feature"> 26610 <section name="feature">
25770 <section name="consensus"> 26623 <section name="consensus">
25771 <param name="sorting_method" value="none"/> 26624 <param name="sorting_method" value="none"/>
25772 <param name="sort_by_maps" value="false"/> 26625 <param name="sort_by_maps" value="false"/>
25773 <param name="sort_by_size" value="false"/> 26626 <param name="sort_by_size" value="false"/>
25774 </section> 26627 </section>
25775 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26628 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25776 <output name="ctd_out" ftype="xml"> 26629 <output name="ctd_out" ftype="xml">
25777 <assert_contents> 26630 <assert_contents>
25778 <is_valid_xml/> 26631 <is_valid_xml/>
25779 </assert_contents> 26632 </assert_contents>
25780 </output> 26633 </output>
25784 <param name="adv_opts_selector" value="advanced"/> 26637 <param name="adv_opts_selector" value="advanced"/>
25785 <param name="force" value="false"/> 26638 <param name="force" value="false"/>
25786 <param name="test" value="true"/> 26639 <param name="test" value="true"/>
25787 </conditional> 26640 </conditional>
25788 <param name="in" value="TextExporter_9_input.idXML"/> 26641 <param name="in" value="TextExporter_9_input.idXML"/>
25789 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> 26642 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
25790 <param name="separator" value=""/> 26643 <param name="separator" value=""/>
25791 <param name="replacement" value="_"/> 26644 <param name="replacement" value="_"/>
25792 <param name="quoting" value="none"/> 26645 <param name="quoting" value="none"/>
25793 <param name="no_ids" value="false"/> 26646 <param name="no_ids" value="false"/>
25794 <section name="feature"> 26647 <section name="feature">
25807 <section name="consensus"> 26660 <section name="consensus">
25808 <param name="sorting_method" value="none"/> 26661 <param name="sorting_method" value="none"/>
25809 <param name="sort_by_maps" value="false"/> 26662 <param name="sort_by_maps" value="false"/>
25810 <param name="sort_by_size" value="false"/> 26663 <param name="sort_by_size" value="false"/>
25811 </section> 26664 </section>
25812 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 26665 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25813 <output name="ctd_out" ftype="xml"> 26666 <output name="ctd_out" ftype="xml">
25814 <assert_contents> 26667 <assert_contents>
25815 <is_valid_xml/> 26668 <is_valid_xml/>
25816 </assert_contents> 26669 </assert_contents>
25817 </output> 26670 </output>
25907 <param name="test" value="true"/> 26760 <param name="test" value="true"/>
25908 </conditional> 26761 </conditional>
25909 <param name="in" value="TOFCalibration_1_input.mzML"/> 26762 <param name="in" value="TOFCalibration_1_input.mzML"/>
25910 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 26763 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25911 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> 26764 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
25912 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/> 26765 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
25913 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/> 26766 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
25914 <param name="peak_data" value="false"/> 26767 <param name="peak_data" value="false"/>
25915 <section name="algorithm"> 26768 <section name="algorithm">
25916 <section name="PeakPicker"> 26769 <section name="PeakPicker">
25917 <param name="signal_to_noise" value="3.0"/> 26770 <param name="signal_to_noise" value="3.0"/>
25918 <param name="centroid_percentage" value="0.6"/> 26771 <param name="centroid_percentage" value="0.6"/>
25989 <param name="test" value="true"/> 26842 <param name="test" value="true"/>
25990 </conditional> 26843 </conditional>
25991 <param name="in" value="TOFCalibration_2_input.mzML"/> 26844 <param name="in" value="TOFCalibration_2_input.mzML"/>
25992 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> 26845 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25993 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> 26846 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
25994 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/> 26847 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
25995 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/> 26848 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
25996 <param name="peak_data" value="true"/> 26849 <param name="peak_data" value="true"/>
25997 <section name="algorithm"> 26850 <section name="algorithm">
25998 <section name="PeakPicker"> 26851 <section name="PeakPicker">
25999 <param name="signal_to_noise" value="3.0"/> 26852 <param name="signal_to_noise" value="3.0"/>
26000 <param name="centroid_percentage" value="0.6"/> 26853 <param name="centroid_percentage" value="0.6"/>
26314 <assert_contents> 27167 <assert_contents>
26315 <is_valid_xml/> 27168 <is_valid_xml/>
26316 </assert_contents> 27169 </assert_contents>
26317 </output> 27170 </output>
26318 </test> 27171 </test>
27172 <test expect_num_outputs="2">
27173 <conditional name="adv_opts_cond">
27174 <param name="adv_opts_selector" value="advanced"/>
27175 <param name="force" value="false"/>
27176 <param name="test" value="true"/>
27177 </conditional>
27178 <param name="in" value="spectra.mzML"/>
27179 <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
27180 <param name="database" value="proteinslong.fasta"/>
27181 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
27182 <param name="ignore_adapter_param" value="false"/>
27183 <param name="precursor_mass_tolerance" value="5.0"/>
27184 <param name="fragment_mass_tolerance" value="0.3"/>
27185 <param name="precursor_error_units" value="ppm"/>
27186 <param name="fragment_error_units" value="Da"/>
27187 <param name="max_precursor_charge" value="0"/>
27188 <param name="no_isotope_error" value="false"/>
27189 <param name="fixed_modifications" value=""/>
27190 <param name="variable_modifications" value="Oxidation (M)"/>
27191 <param name="minimum_fragment_mz" value="150.0"/>
27192 <param name="enzyme" value="Trypsin"/>
27193 <param name="missed_cleavages" value="1"/>
27194 <param name="semi_cleavage" value="false"/>
27195 <param name="output_results" value="all"/>
27196 <param name="max_valid_expect" value="0.1"/>
27197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
27198 <output name="ctd_out" ftype="xml">
27199 <assert_contents>
27200 <is_valid_xml/>
27201 </assert_contents>
27202 </output>
27203 </test>
26319 </xml> 27204 </xml>
26320 <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> 27205 <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>