Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer
comparison macros_autotest.xml @ 11:b1a8601e2ea0 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
---|---|
date | Tue, 13 Oct 2020 20:04:00 +0000 |
parents | 416fc18f347a |
children |
comparison
equal
deleted
inserted
replaced
10:416fc18f347a | 11:b1a8601e2ea0 |
---|---|
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=(?<SCAN>\d+)"/> | 11498 <param name="scan_regex" value="scan=(?<SCAN>\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=""Q9HP81""/> | |
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=""Carboxymethyl (C)""/> | 16326 <param name="modifications" value=""Carboxymethyl (C)""/> |
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=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> | 16418 <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> |
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=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> | |
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=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> | |
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> |