Mercurial > repos > galaxyp > openms_fuzzydiff
comparison macros_autotest.xml @ 13:ed9a839cbbda draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:10:05 +0000 |
| parents | 55f3c74f6ce6 |
| children |
comparison
equal
deleted
inserted
replaced
| 12:55f3c74f6ce6 | 13:ed9a839cbbda |
|---|---|
| 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> |