Mercurial > repos > galaxyp > openms_msfraggeradapter

comparison macros_autotest.xml @ 4:1ad0d0fd8696 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 14 Dec 2020 08:29:51 +0000
parents a51cf27d4b5c
children
comparison
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3:1576fcc8a5fc 4:1ad0d0fd8696
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"/>
25470 <param name="force" value="false"/> 25461 <param name="force" value="false"/>
25471 <param name="test" value="true"/> 25462 <param name="test" value="true"/>
25472 </conditional> 25463 </conditional>
25473 <param name="in" value="SiriusAdapter_1_input.mzML"/> 25464 <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"/> 25465 <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"> 25466 <section name="preprocessing">
25477 <param name="filter_by_num_masstraces" value="1"/> 25467 <param name="filter_by_num_masstraces" value="1"/>
25478 <param name="precursor_mz_tolerance" value="0.005"/> 25468 <param name="precursor_mz_tolerance" value="0.005"/>
25479 <param name="precursor_mz_tolerance_unit" value="Da"/> 25469 <param name="precursor_mz_tolerance_unit" value="Da"/>
25480 <param name="precursor_rt_tolerance" value="5"/> 25470 <param name="precursor_rt_tolerance" value="5"/>
25513 <param name="test" value="true"/> 25503 <param name="test" value="true"/>
25514 </conditional> 25504 </conditional>
25515 <param name="in" value="SiriusAdapter_2_input.mzML"/> 25505 <param name="in" value="SiriusAdapter_2_input.mzML"/>
25516 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> 25506 <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"/> 25507 <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"> 25508 <section name="preprocessing">
25520 <param name="filter_by_num_masstraces" value="3"/> 25509 <param name="filter_by_num_masstraces" value="3"/>
25521 <param name="precursor_mz_tolerance" value="0.005"/> 25510 <param name="precursor_mz_tolerance" value="0.005"/>
25522 <param name="precursor_mz_tolerance_unit" value="Da"/> 25511 <param name="precursor_mz_tolerance_unit" value="Da"/>
25523 <param name="precursor_rt_tolerance" value="5"/> 25512 <param name="precursor_rt_tolerance" value="5"/>
25556 <param name="test" value="true"/> 25545 <param name="test" value="true"/>
25557 </conditional> 25546 </conditional>
25558 <param name="in" value="SiriusAdapter_3_input.mzML"/> 25547 <param name="in" value="SiriusAdapter_3_input.mzML"/>
25559 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> 25548 <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"/> 25549 <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"> 25550 <section name="preprocessing">
25563 <param name="filter_by_num_masstraces" value="3"/> 25551 <param name="filter_by_num_masstraces" value="3"/>
25564 <param name="precursor_mz_tolerance" value="0.005"/> 25552 <param name="precursor_mz_tolerance" value="0.005"/>
25565 <param name="precursor_mz_tolerance_unit" value="Da"/> 25553 <param name="precursor_mz_tolerance_unit" value="Da"/>
25566 <param name="precursor_rt_tolerance" value="5"/> 25554 <param name="precursor_rt_tolerance" value="5"/>
25599 <param name="test" value="true"/> 25587 <param name="test" value="true"/>
25600 </conditional> 25588 </conditional>
25601 <param name="in" value="SiriusAdapter_3_input.mzML"/> 25589 <param name="in" value="SiriusAdapter_3_input.mzML"/>
25602 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> 25590 <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"/> 25591 <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"> 25592 <section name="preprocessing">
25606 <param name="filter_by_num_masstraces" value="1"/> 25593 <param name="filter_by_num_masstraces" value="1"/>
25607 <param name="precursor_mz_tolerance" value="0.005"/> 25594 <param name="precursor_mz_tolerance" value="0.005"/>
25608 <param name="precursor_mz_tolerance_unit" value="Da"/> 25595 <param name="precursor_mz_tolerance_unit" value="Da"/>
25609 <param name="precursor_rt_tolerance" value="5"/> 25596 <param name="precursor_rt_tolerance" value="5"/>
25642 <param name="test" value="true"/> 25629 <param name="test" value="true"/>
25643 </conditional> 25630 </conditional>
25644 <param name="in" value="SiriusAdapter_4_input.mzML"/> 25631 <param name="in" value="SiriusAdapter_4_input.mzML"/>
25645 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> 25632 <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"/> 25633 <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"> 25634 <section name="preprocessing">
25649 <param name="filter_by_num_masstraces" value="1"/> 25635 <param name="filter_by_num_masstraces" value="1"/>
25650 <param name="precursor_mz_tolerance" value="0.005"/> 25636 <param name="precursor_mz_tolerance" value="0.005"/>
25651 <param name="precursor_mz_tolerance_unit" value="Da"/> 25637 <param name="precursor_mz_tolerance_unit" value="Da"/>
25652 <param name="precursor_rt_tolerance" value="5"/> 25638 <param name="precursor_rt_tolerance" value="5"/>
25685 <param name="test" value="true"/> 25671 <param name="test" value="true"/>
25686 </conditional> 25672 </conditional>
25687 <param name="in" value="SiriusAdapter_4_input.mzML"/> 25673 <param name="in" value="SiriusAdapter_4_input.mzML"/>
25688 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> 25674 <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"/> 25675 <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"> 25676 <section name="preprocessing">
25692 <param name="filter_by_num_masstraces" value="1"/> 25677 <param name="filter_by_num_masstraces" value="1"/>
25693 <param name="precursor_mz_tolerance" value="0.005"/> 25678 <param name="precursor_mz_tolerance" value="0.005"/>
25694 <param name="precursor_mz_tolerance_unit" value="Da"/> 25679 <param name="precursor_mz_tolerance_unit" value="Da"/>
25695 <param name="precursor_rt_tolerance" value="5"/> 25680 <param name="precursor_rt_tolerance" value="5"/>
25729 </conditional> 25714 </conditional>
25730 <param name="in" value="SiriusAdapter_2_input.mzML"/> 25715 <param name="in" value="SiriusAdapter_2_input.mzML"/>
25731 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> 25716 <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"/> 25717 <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"/> 25718 <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"> 25719 <section name="preprocessing">
25736 <param name="filter_by_num_masstraces" value="1"/> 25720 <param name="filter_by_num_masstraces" value="1"/>
25737 <param name="precursor_mz_tolerance" value="0.005"/> 25721 <param name="precursor_mz_tolerance" value="0.005"/>
25738 <param name="precursor_mz_tolerance_unit" value="Da"/> 25722 <param name="precursor_mz_tolerance_unit" value="Da"/>
25739 <param name="precursor_rt_tolerance" value="5"/> 25723 <param name="precursor_rt_tolerance" value="5"/>
27200 <is_valid_xml/> 27184 <is_valid_xml/>
27201 </assert_contents> 27185 </assert_contents>
27202 </output> 27186 </output>
27203 </test> 27187 </test>
27204 </xml> 27188 </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> 27189 <xml name="autotest_InspectAdapter"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_RTPredict"/><xml name="autotest_PTPredict"/><xml name="autotest_IDDecoyProbability"/></macros>