Mercurial > repos > galaxyp > openms_cometadapter
comparison macros_autotest.xml @ 5:704cace078c4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3cafa1cc1ea87eb7a0dc0e7aae013780c3565178"
| author | galaxyp |
|---|---|
| date | Sat, 05 Dec 2020 19:51:29 +0000 |
| parents | bf9bd980f729 |
| children | 75e0c261bd1a |
comparison
equal
deleted
inserted
replaced
| 4:1533239ed6f2 | 5:704cace078c4 |
|---|---|
| 124 <param name="use_known_unknowns" value="false"/> | 124 <param name="use_known_unknowns" value="false"/> |
| 125 <param name="min_transitions" value="1"/> | 125 <param name="min_transitions" value="1"/> |
| 126 <param name="max_transitions" value="3"/> | 126 <param name="max_transitions" value="3"/> |
| 127 <param name="cosine_similarity_threshold" value="0.98"/> | 127 <param name="cosine_similarity_threshold" value="0.98"/> |
| 128 <param name="transition_threshold" value="5.0"/> | 128 <param name="transition_threshold" value="5.0"/> |
| 129 <param name="out_workspace_directory" value=""/> | |
| 130 <section name="deisotoping"> | 129 <section name="deisotoping"> |
| 131 <param name="use_deisotoper" value="false"/> | 130 <param name="use_deisotoper" value="false"/> |
| 132 <param name="fragment_tolerance" value="1.0"/> | 131 <param name="fragment_tolerance" value="1.0"/> |
| 133 <param name="fragment_unit" value="ppm"/> | 132 <param name="fragment_unit" value="ppm"/> |
| 134 <param name="min_charge" value="1"/> | 133 <param name="min_charge" value="1"/> |
| 193 <param name="use_known_unknowns" value="false"/> | 192 <param name="use_known_unknowns" value="false"/> |
| 194 <param name="min_transitions" value="1"/> | 193 <param name="min_transitions" value="1"/> |
| 195 <param name="max_transitions" value="3"/> | 194 <param name="max_transitions" value="3"/> |
| 196 <param name="cosine_similarity_threshold" value="0.98"/> | 195 <param name="cosine_similarity_threshold" value="0.98"/> |
| 197 <param name="transition_threshold" value="5.0"/> | 196 <param name="transition_threshold" value="5.0"/> |
| 198 <param name="out_workspace_directory" value=""/> | |
| 199 <section name="deisotoping"> | 197 <section name="deisotoping"> |
| 200 <param name="use_deisotoper" value="false"/> | 198 <param name="use_deisotoper" value="false"/> |
| 201 <param name="fragment_tolerance" value="1.0"/> | 199 <param name="fragment_tolerance" value="1.0"/> |
| 202 <param name="fragment_unit" value="ppm"/> | 200 <param name="fragment_unit" value="ppm"/> |
| 203 <param name="min_charge" value="1"/> | 201 <param name="min_charge" value="1"/> |
| 262 <param name="use_known_unknowns" value="false"/> | 260 <param name="use_known_unknowns" value="false"/> |
| 263 <param name="min_transitions" value="1"/> | 261 <param name="min_transitions" value="1"/> |
| 264 <param name="max_transitions" value="3"/> | 262 <param name="max_transitions" value="3"/> |
| 265 <param name="cosine_similarity_threshold" value="0.98"/> | 263 <param name="cosine_similarity_threshold" value="0.98"/> |
| 266 <param name="transition_threshold" value="5.0"/> | 264 <param name="transition_threshold" value="5.0"/> |
| 267 <param name="out_workspace_directory" value=""/> | |
| 268 <section name="deisotoping"> | 265 <section name="deisotoping"> |
| 269 <param name="use_deisotoper" value="false"/> | 266 <param name="use_deisotoper" value="false"/> |
| 270 <param name="fragment_tolerance" value="1.0"/> | 267 <param name="fragment_tolerance" value="1.0"/> |
| 271 <param name="fragment_unit" value="ppm"/> | 268 <param name="fragment_unit" value="ppm"/> |
| 272 <param name="min_charge" value="1"/> | 269 <param name="min_charge" value="1"/> |
| 331 <param name="use_known_unknowns" value="false"/> | 328 <param name="use_known_unknowns" value="false"/> |
| 332 <param name="min_transitions" value="1"/> | 329 <param name="min_transitions" value="1"/> |
| 333 <param name="max_transitions" value="3"/> | 330 <param name="max_transitions" value="3"/> |
| 334 <param name="cosine_similarity_threshold" value="0.98"/> | 331 <param name="cosine_similarity_threshold" value="0.98"/> |
| 335 <param name="transition_threshold" value="5.0"/> | 332 <param name="transition_threshold" value="5.0"/> |
| 336 <param name="out_workspace_directory" value=""/> | |
| 337 <section name="deisotoping"> | 333 <section name="deisotoping"> |
| 338 <param name="use_deisotoper" value="false"/> | 334 <param name="use_deisotoper" value="false"/> |
| 339 <param name="fragment_tolerance" value="1.0"/> | 335 <param name="fragment_tolerance" value="1.0"/> |
| 340 <param name="fragment_unit" value="ppm"/> | 336 <param name="fragment_unit" value="ppm"/> |
| 341 <param name="min_charge" value="1"/> | 337 <param name="min_charge" value="1"/> |
| 400 <param name="use_known_unknowns" value="true"/> | 396 <param name="use_known_unknowns" value="true"/> |
| 401 <param name="min_transitions" value="1"/> | 397 <param name="min_transitions" value="1"/> |
| 402 <param name="max_transitions" value="3"/> | 398 <param name="max_transitions" value="3"/> |
| 403 <param name="cosine_similarity_threshold" value="0.98"/> | 399 <param name="cosine_similarity_threshold" value="0.98"/> |
| 404 <param name="transition_threshold" value="5.0"/> | 400 <param name="transition_threshold" value="5.0"/> |
| 405 <param name="out_workspace_directory" value=""/> | |
| 406 <section name="deisotoping"> | 401 <section name="deisotoping"> |
| 407 <param name="use_deisotoper" value="false"/> | 402 <param name="use_deisotoper" value="false"/> |
| 408 <param name="fragment_tolerance" value="1.0"/> | 403 <param name="fragment_tolerance" value="1.0"/> |
| 409 <param name="fragment_unit" value="ppm"/> | 404 <param name="fragment_unit" value="ppm"/> |
| 410 <param name="min_charge" value="1"/> | 405 <param name="min_charge" value="1"/> |
| 469 <param name="use_known_unknowns" value="false"/> | 464 <param name="use_known_unknowns" value="false"/> |
| 470 <param name="min_transitions" value="2"/> | 465 <param name="min_transitions" value="2"/> |
| 471 <param name="max_transitions" value="3"/> | 466 <param name="max_transitions" value="3"/> |
| 472 <param name="cosine_similarity_threshold" value="0.98"/> | 467 <param name="cosine_similarity_threshold" value="0.98"/> |
| 473 <param name="transition_threshold" value="3.0"/> | 468 <param name="transition_threshold" value="3.0"/> |
| 474 <param name="out_workspace_directory" value=""/> | |
| 475 <section name="deisotoping"> | 469 <section name="deisotoping"> |
| 476 <param name="use_deisotoper" value="false"/> | 470 <param name="use_deisotoper" value="false"/> |
| 477 <param name="fragment_tolerance" value="1.0"/> | 471 <param name="fragment_tolerance" value="1.0"/> |
| 478 <param name="fragment_unit" value="ppm"/> | 472 <param name="fragment_unit" value="ppm"/> |
| 479 <param name="min_charge" value="1"/> | 473 <param name="min_charge" value="1"/> |
| 538 <param name="use_known_unknowns" value="true"/> | 532 <param name="use_known_unknowns" value="true"/> |
| 539 <param name="min_transitions" value="2"/> | 533 <param name="min_transitions" value="2"/> |
| 540 <param name="max_transitions" value="3"/> | 534 <param name="max_transitions" value="3"/> |
| 541 <param name="cosine_similarity_threshold" value="0.98"/> | 535 <param name="cosine_similarity_threshold" value="0.98"/> |
| 542 <param name="transition_threshold" value="3.0"/> | 536 <param name="transition_threshold" value="3.0"/> |
| 543 <param name="out_workspace_directory" value=""/> | |
| 544 <section name="deisotoping"> | 537 <section name="deisotoping"> |
| 545 <param name="use_deisotoper" value="false"/> | 538 <param name="use_deisotoper" value="false"/> |
| 546 <param name="fragment_tolerance" value="1.0"/> | 539 <param name="fragment_tolerance" value="1.0"/> |
| 547 <param name="fragment_unit" value="ppm"/> | 540 <param name="fragment_unit" value="ppm"/> |
| 548 <param name="min_charge" value="1"/> | 541 <param name="min_charge" value="1"/> |
| 607 <param name="use_known_unknowns" value="false"/> | 600 <param name="use_known_unknowns" value="false"/> |
| 608 <param name="min_transitions" value="2"/> | 601 <param name="min_transitions" value="2"/> |
| 609 <param name="max_transitions" value="3"/> | 602 <param name="max_transitions" value="3"/> |
| 610 <param name="cosine_similarity_threshold" value="0.98"/> | 603 <param name="cosine_similarity_threshold" value="0.98"/> |
| 611 <param name="transition_threshold" value="3.0"/> | 604 <param name="transition_threshold" value="3.0"/> |
| 612 <param name="out_workspace_directory" value=""/> | |
| 613 <section name="deisotoping"> | 605 <section name="deisotoping"> |
| 614 <param name="use_deisotoper" value="false"/> | 606 <param name="use_deisotoper" value="false"/> |
| 615 <param name="fragment_tolerance" value="1.0"/> | 607 <param name="fragment_tolerance" value="1.0"/> |
| 616 <param name="fragment_unit" value="ppm"/> | 608 <param name="fragment_unit" value="ppm"/> |
| 617 <param name="min_charge" value="1"/> | 609 <param name="min_charge" value="1"/> |
| 676 <param name="use_known_unknowns" value="false"/> | 668 <param name="use_known_unknowns" value="false"/> |
| 677 <param name="min_transitions" value="2"/> | 669 <param name="min_transitions" value="2"/> |
| 678 <param name="max_transitions" value="3"/> | 670 <param name="max_transitions" value="3"/> |
| 679 <param name="cosine_similarity_threshold" value="0.98"/> | 671 <param name="cosine_similarity_threshold" value="0.98"/> |
| 680 <param name="transition_threshold" value="3.0"/> | 672 <param name="transition_threshold" value="3.0"/> |
| 681 <param name="out_workspace_directory" value=""/> | |
| 682 <section name="deisotoping"> | 673 <section name="deisotoping"> |
| 683 <param name="use_deisotoper" value="false"/> | 674 <param name="use_deisotoper" value="false"/> |
| 684 <param name="fragment_tolerance" value="1.0"/> | 675 <param name="fragment_tolerance" value="1.0"/> |
| 685 <param name="fragment_unit" value="ppm"/> | 676 <param name="fragment_unit" value="ppm"/> |
| 686 <param name="min_charge" value="1"/> | 677 <param name="min_charge" value="1"/> |
| 24817 <is_valid_xml/> | 24808 <is_valid_xml/> |
| 24818 </assert_contents> | 24809 </assert_contents> |
| 24819 </output> | 24810 </output> |
| 24820 </test> | 24811 </test> |
| 24821 </xml> | 24812 </xml> |
| 24813 <xml name="autotest_PSMFeatureExtractor_org"> | |
| 24814 </xml> | |
| 24822 <xml name="autotest_PSMFeatureExtractor"> | 24815 <xml name="autotest_PSMFeatureExtractor"> |
| 24823 </xml> | 24816 </xml> |
| 24824 <xml name="autotest_PTModel"> | 24817 <xml name="autotest_PTModel"> |
| 24825 <test expect_num_outputs="2"> | 24818 <test expect_num_outputs="2"> |
| 24826 <conditional name="adv_opts_cond"> | 24819 <conditional name="adv_opts_cond"> |
| 25470 <param name="force" value="false"/> | 25463 <param name="force" value="false"/> |
| 25471 <param name="test" value="true"/> | 25464 <param name="test" value="true"/> |
| 25472 </conditional> | 25465 </conditional> |
| 25473 <param name="in" value="SiriusAdapter_1_input.mzML"/> | 25466 <param name="in" value="SiriusAdapter_1_input.mzML"/> |
| 25474 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | 25467 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25475 <param name="out_workspace_directory" value=""/> | |
| 25476 <section name="preprocessing"> | 25468 <section name="preprocessing"> |
| 25477 <param name="filter_by_num_masstraces" value="1"/> | 25469 <param name="filter_by_num_masstraces" value="1"/> |
| 25478 <param name="precursor_mz_tolerance" value="0.005"/> | 25470 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25479 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25471 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25480 <param name="precursor_rt_tolerance" value="5"/> | 25472 <param name="precursor_rt_tolerance" value="5"/> |
| 25513 <param name="test" value="true"/> | 25505 <param name="test" value="true"/> |
| 25514 </conditional> | 25506 </conditional> |
| 25515 <param name="in" value="SiriusAdapter_2_input.mzML"/> | 25507 <param name="in" value="SiriusAdapter_2_input.mzML"/> |
| 25516 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> | 25508 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> |
| 25517 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | 25509 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25518 <param name="out_workspace_directory" value=""/> | |
| 25519 <section name="preprocessing"> | 25510 <section name="preprocessing"> |
| 25520 <param name="filter_by_num_masstraces" value="3"/> | 25511 <param name="filter_by_num_masstraces" value="3"/> |
| 25521 <param name="precursor_mz_tolerance" value="0.005"/> | 25512 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25522 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25513 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25523 <param name="precursor_rt_tolerance" value="5"/> | 25514 <param name="precursor_rt_tolerance" value="5"/> |
| 25556 <param name="test" value="true"/> | 25547 <param name="test" value="true"/> |
| 25557 </conditional> | 25548 </conditional> |
| 25558 <param name="in" value="SiriusAdapter_3_input.mzML"/> | 25549 <param name="in" value="SiriusAdapter_3_input.mzML"/> |
| 25559 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> | 25550 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> |
| 25560 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | 25551 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25561 <param name="out_workspace_directory" value=""/> | |
| 25562 <section name="preprocessing"> | 25552 <section name="preprocessing"> |
| 25563 <param name="filter_by_num_masstraces" value="3"/> | 25553 <param name="filter_by_num_masstraces" value="3"/> |
| 25564 <param name="precursor_mz_tolerance" value="0.005"/> | 25554 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25565 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25555 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25566 <param name="precursor_rt_tolerance" value="5"/> | 25556 <param name="precursor_rt_tolerance" value="5"/> |
| 25599 <param name="test" value="true"/> | 25589 <param name="test" value="true"/> |
| 25600 </conditional> | 25590 </conditional> |
| 25601 <param name="in" value="SiriusAdapter_3_input.mzML"/> | 25591 <param name="in" value="SiriusAdapter_3_input.mzML"/> |
| 25602 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> | 25592 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> |
| 25603 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> | 25593 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> |
| 25604 <param name="out_workspace_directory" value=""/> | |
| 25605 <section name="preprocessing"> | 25594 <section name="preprocessing"> |
| 25606 <param name="filter_by_num_masstraces" value="1"/> | 25595 <param name="filter_by_num_masstraces" value="1"/> |
| 25607 <param name="precursor_mz_tolerance" value="0.005"/> | 25596 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25608 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25597 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25609 <param name="precursor_rt_tolerance" value="5"/> | 25598 <param name="precursor_rt_tolerance" value="5"/> |
| 25642 <param name="test" value="true"/> | 25631 <param name="test" value="true"/> |
| 25643 </conditional> | 25632 </conditional> |
| 25644 <param name="in" value="SiriusAdapter_4_input.mzML"/> | 25633 <param name="in" value="SiriusAdapter_4_input.mzML"/> |
| 25645 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> | 25634 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> |
| 25646 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> | 25635 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> |
| 25647 <param name="out_workspace_directory" value=""/> | |
| 25648 <section name="preprocessing"> | 25636 <section name="preprocessing"> |
| 25649 <param name="filter_by_num_masstraces" value="1"/> | 25637 <param name="filter_by_num_masstraces" value="1"/> |
| 25650 <param name="precursor_mz_tolerance" value="0.005"/> | 25638 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25651 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25639 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25652 <param name="precursor_rt_tolerance" value="5"/> | 25640 <param name="precursor_rt_tolerance" value="5"/> |
| 25685 <param name="test" value="true"/> | 25673 <param name="test" value="true"/> |
| 25686 </conditional> | 25674 </conditional> |
| 25687 <param name="in" value="SiriusAdapter_4_input.mzML"/> | 25675 <param name="in" value="SiriusAdapter_4_input.mzML"/> |
| 25688 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> | 25676 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> |
| 25689 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | 25677 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25690 <param name="out_workspace_directory" value=""/> | |
| 25691 <section name="preprocessing"> | 25678 <section name="preprocessing"> |
| 25692 <param name="filter_by_num_masstraces" value="1"/> | 25679 <param name="filter_by_num_masstraces" value="1"/> |
| 25693 <param name="precursor_mz_tolerance" value="0.005"/> | 25680 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25694 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25681 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25695 <param name="precursor_rt_tolerance" value="5"/> | 25682 <param name="precursor_rt_tolerance" value="5"/> |
| 25729 </conditional> | 25716 </conditional> |
| 25730 <param name="in" value="SiriusAdapter_2_input.mzML"/> | 25717 <param name="in" value="SiriusAdapter_2_input.mzML"/> |
| 25731 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> | 25718 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> |
| 25732 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> | 25719 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25733 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> | 25720 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> |
| 25734 <param name="out_workspace_directory" value=""/> | |
| 25735 <section name="preprocessing"> | 25721 <section name="preprocessing"> |
| 25736 <param name="filter_by_num_masstraces" value="1"/> | 25722 <param name="filter_by_num_masstraces" value="1"/> |
| 25737 <param name="precursor_mz_tolerance" value="0.005"/> | 25723 <param name="precursor_mz_tolerance" value="0.005"/> |
| 25738 <param name="precursor_mz_tolerance_unit" value="Da"/> | 25724 <param name="precursor_mz_tolerance_unit" value="Da"/> |
| 25739 <param name="precursor_rt_tolerance" value="5"/> | 25725 <param name="precursor_rt_tolerance" value="5"/> |
| 27200 <is_valid_xml/> | 27186 <is_valid_xml/> |
| 27201 </assert_contents> | 27187 </assert_contents> |
| 27202 </output> | 27188 </output> |
| 27203 </test> | 27189 </test> |
| 27204 </xml> | 27190 </xml> |
| 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> | 27191 <xml name="autotest_RTPredict"/><xml name="autotest_InspectAdapter"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_PTPredict"/></macros> |