Mercurial > repos > galaxyp > msconvert

comparison msconvert_macros.xml @ 11:052798dd73dd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
author galaxyp
date Mon, 30 Nov 2020 16:00:27 +0000
parents 06747cba5685
children 5e94d5403baf
comparison
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10:06747cba5685 11:052798dd73dd
1 <macros> 1 <macros>
2 <token name="@VERSION@">3.0.19052</token> 2 <token name="@VERSION@">3.0.20287</token>
3 <token name="@FULL_VERSION@">@VERSION@-089e81090</token> 3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
4
5 <xml name="msconvertCommand"> 4 <xml name="msconvertCommand">
6 <command detect_errors="exit_code"> 5 <command detect_errors="exit_code">
7 <![CDATA[ 6 <![CDATA[
8 #import re 7 #import re
9 #set $ext = $input.ext 8 #set $ext = $input.ext
37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) 36 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' 37 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && 38 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
40 #end if 39 #end if
41 40
42 41 CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) &&
43 CAN_SUDO=\$(sudo -n -l 2> /dev/null; echo \$?) &&
44 if [ "\$CAN_SUDO" -eq "0" ]; then 42 if [ "\$CAN_SUDO" -eq "0" ]; then
45 uid=`id -u` && 43 uid=`id -u` &&
46 gid=`id -g` && 44 gid=`id -g` &&
47 WINE="wine64_anyuser"; 45 WINE="wine64_anyuser";
48 else 46 else
49 WINE="wine64" && 47 WINE="wine64" &&
50 ## create a writable copy of wine prefix (since copying fails for some html 48 ## create a writable copy of wine prefix (since copying fails for some html
51 ## stderr and exit code is swallowed) 49 ## stderr and exit code is swallowed)
52 export WINEPREFIX=\$(mktemp -d) && 50 export WINEPREFIX=\$(mktemp -d) &&
53 (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true); 51 (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
54 fi 52 fi
55 && 53 &&
56 \$WINE msconvert ${inputmask} 54 \$WINE msconvert ${inputmask}
57 55
58 --outdir outputs 56 --outdir outputs
212 --gzip 210 --gzip
213 #end if 211 #end if
214 212
215 #if $general_options.multi_run_output.do_multi_run_output == 'false': 213 #if $general_options.multi_run_output.do_multi_run_output == 'false':
216 --outfile '${os.path.splitext($basename)[0]}' 214 --outfile '${os.path.splitext($basename)[0]}'
217 && 215 #end if
218 if [ "\$CAN_SUDO" -eq "0" ]; then 216 &&
219 sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' && 217 if [ "\$CAN_SUDO" -eq "0" ]; then
220 sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; 218 sudo chown -R \$uid:\$gid './';
221 else 219 fi
222 mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; 220 #if $general_options.multi_run_output.do_multi_run_output == 'false':
223 fi 221 && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
224 #else 222 #else
225 && ls -la outputs/ 223 ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
224 ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
225 #if $output_type == 'mzML' or $output_type == 'mzXML'
226 && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
227 ## a newline is needed after `#echo ...` therefore the `;'` on the next line
228 ;'
229 #end if
226 #end if 230 #end if
227 231
228 #if $data_processing.precursor_refinement.use_mzrefinement 232 #if $data_processing.precursor_refinement.use_mzrefinement
229 && if [ "\$CAN_SUDO" -ne "0" ]; then 233 && mv '$output_refinement_name' '$output_refinement';
230 mv '$output_refinement_name' '$output_refinement';
231 fi
232 #end if 234 #end if
233 ]]> 235 ]]>
234 </command> 236 </command>
235 </xml> 237 </xml>
236 238
541 </xml> 543 </xml>
542 544
543 545
544 <xml name="msconvert_tests"> 546 <xml name="msconvert_tests">
545 <test> 547 <test>
546 <param name="input" value="small.mzML" /> 548 <param name="input" value="small.mzML" ftype="mzml" />
547 <param name="license_agreement" value="true" /> 549 <param name="license_agreement" value="true" />
548 <param name="output_type" value="mzML" /> 550 <param name="output_type" value="mzML" />
549 <param name="pick_peaks" value="true" /> 551 <param name="pick_peaks" value="true" />
550 <param name="pick_peaks_algorithm" value="cwt" /> 552 <param name="pick_peaks_algorithm" value="cwt" />
551 <param name="pick_peaks_ms_levels" value="1-" /> 553 <param name="pick_peaks_ms_levels" value="1-" />
552 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> 554 <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
553 </test> 555 </test>
554 <test> 556 <test>
555 <param name="input" value="small.RAW" ftype="thermo.raw" /> 557 <param name="input" value="small.RAW" ftype="thermo.raw" />
556 <param name="license_agreement" value="true" /> 558 <param name="license_agreement" value="true" />
557 <param name="output_type" value="mzML" /> 559 <param name="output_type" value="mzML" />
558 <param name="pick_peaks" value="true" /> 560 <param name="pick_peaks" value="true" />
559 <param name="pick_peaks_algorithm" value="vendor" /> 561 <param name="pick_peaks_algorithm" value="vendor" />
560 <param name="pick_peaks_ms_levels" value="1-" /> 562 <param name="pick_peaks_ms_levels" value="1-" />
561 <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" /> 563 <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
562 </test> 564 </test>
563 <test> 565 <test>
564 <param name="input" value="ThyroglobMRM000003.d.tar" /> 566 <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
565 <param name="license_agreement" value="true" /> 567 <param name="license_agreement" value="true" />
566 <param name="output_type" value="mzML" /> 568 <param name="output_type" value="mzML" />
567 <param name="combineIonMobilitySpectra" value="true" /> 569 <param name="combineIonMobilitySpectra" value="true" />
568 <param name="do_scan_summing" value="true" /> 570 <param name="do_scan_summing" value="true" />
569 <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" /> 571 <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
570 </test> 572 </test>
571 <test> 573 <test>
572 <param name="input" value="MassLynxTest.raw.tar" /> 574 <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
573 <param name="license_agreement" value="true" /> 575 <param name="license_agreement" value="true" />
574 <param name="output_type" value="mzML" /> 576 <param name="output_type" value="mzML" />
575 <output name="output" file="MassLynxTest.mzML" lines_diff="4" /> 577 <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
576 </test> 578 </test>
577 <test> 579 <test>
578 <param name="input" value="AgilentMassHunterTest.d.tar" /> 580 <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
579 <param name="license_agreement" value="true" /> 581 <param name="license_agreement" value="true" />
580 <param name="output_type" value="mzXML" /> 582 <param name="output_type" value="mzXML" />
581 <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" /> 583 <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
582 </test> 584 </test>
583 <test> 585 <test>
584 <param name="input" value="BrukerBafTest.d.tar" /> 586 <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
585 <param name="license_agreement" value="true" /> 587 <param name="license_agreement" value="true" />
586 <param name="output_type" value="mzML" /> 588 <param name="output_type" value="mzML" />
587 <param name="pick_peaks" value="true" /> 589 <param name="pick_peaks" value="true" />
588 <param name="pick_peaks_algorithm" value="vendor" /> 590 <param name="pick_peaks_algorithm" value="vendor" />
589 <param name="pick_peaks_ms_levels" value="1-" /> 591 <param name="pick_peaks_ms_levels" value="1-" />
590 <output name="output" file="BrukerBafTest.mzML" lines_diff="4" /> 592 <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
591 </test> 593 </test>
592 <test> 594 <test>
593 <param name="input" value="SciexTest.wiff.tar" /> 595 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
594 <param name="license_agreement" value="true" /> 596 <param name="license_agreement" value="true" />
595 <param name="output_type" value="mzML" /> 597 <param name="output_type" value="mzML" />
596 <param name="do_multi_run_output" value="false" /> 598 <param name="do_multi_run_output" value="false" />
597 <param name="runIndexSet" value="0" /> 599 <param name="runIndexSet" value="0" />
598 <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" /> 600 <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
599 </test> 601 </test>
600 <test> 602 <test>
601 <param name="input" value="SciexTest.wiff.tar" /> 603 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
602 <param name="license_agreement" value="true" /> 604 <param name="license_agreement" value="true" />
603 <param name="output_type" value="mzXML" /> 605 <param name="output_type" value="mzXML" />
604 <param name="do_multi_run_output" value="false" /> 606 <param name="do_multi_run_output" value="false" />
605 <param name="runIndexSet" value="0" /> 607 <param name="runIndexSet" value="0" />
606 <param name="indices_0|from" value="0" /> 608 <param name="indices_0|from" value="0" />
607 <param name="indices_0|to" value="499" /> 609 <param name="indices_0|to" value="499" />
608 <param name="srmAsSpectra" value="true" /> 610 <param name="srmAsSpectra" value="true" />
609 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" /> 611 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
610 </test> 612 </test>
611 <test> 613 <test>
612 <param name="input" value="SciexTest.wiff.tar" /> 614 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
613 <param name="license_agreement" value="true" /> 615 <param name="license_agreement" value="true" />
614 <param name="output_type" value="mzXML" /> 616 <param name="output_type" value="mzXML" />
615 <param name="do_multi_run_output" value="false" /> 617 <param name="do_multi_run_output" value="false" />
616 <param name="runIndexSet" value="1" /> 618 <param name="runIndexSet" value="1" />
617 <param name="indices_0|from" value="0" /> 619 <param name="indices_0|from" value="0" />
618 <param name="indices_0|to" value="499" /> 620 <param name="indices_0|to" value="499" />
619 <param name="srmAsSpectra" value="true" /> 621 <param name="srmAsSpectra" value="true" />
620 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" /> 622 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
621 </test> 623 </test>
622 <test> 624 <test>
623 <param name="input" value="SciexTest.wiff.tar" /> 625 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
624 <param name="license_agreement" value="true" /> 626 <param name="license_agreement" value="true" />
625 <param name="output_type" value="mzML" /> 627 <param name="output_type" value="mzML" />
626 <param name="do_multi_run_output" value="true" /> 628 <param name="do_multi_run_output" value="true" />
627 <param name="run_index_set_0|from" value="0" /> 629 <param name="run_index_set_0|from" value="0" />
628 <param name="run_index_set_0|to" value="1" /> 630 <param name="run_index_set_0|to" value="1" />
629 <output_collection name="multi_run_output_list" type="list"> 631 <output_collection name="multi_run_output_list" type="list">
630 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> 632 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
631 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> 633 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
632 </output_collection> 634 </output_collection>
633 </test> 635 </test>
634 <test> 636 <test>
635 <param name="input" value="SciexTest.wiff.tar" /> 637 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
636 <param name="license_agreement" value="true" /> 638 <param name="license_agreement" value="true" />
637 <param name="output_type" value="mzML" /> 639 <param name="output_type" value="mzML" />
638 <param name="do_multi_run_output" value="true" /> 640 <param name="do_multi_run_output" value="true" />
639 <output_collection name="multi_run_output_list" type="list"> 641 <output_collection name="multi_run_output_list" type="list">
640 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> 642 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
641 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> 643 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
642 </output_collection> 644 </output_collection>
643 </test> 645 </test>
644 646
645 <!-- this data file only has profile MS1, so the result is the same --> 647 <!-- this data file only has profile MS1, so the result is the same -->
646 <test> 648 <test>
647 <param name="input" value="small.mzML" /> 649 <param name="input" value="small.mzML" ftype="mzml" />
648 <param name="license_agreement" value="true" /> 650 <param name="license_agreement" value="true" />
649 <param name="output_type" value="mzML" /> 651 <param name="output_type" value="mzML" />
650 <param name="pick_peaks" value="true" /> 652 <param name="pick_peaks" value="true" />
651 <param name="pick_peaks_algorithm" value="cwt" /> 653 <param name="pick_peaks_algorithm" value="cwt" />
652 <param name="pick_peaks_ms_levels" value="1" /> 654 <param name="pick_peaks_ms_levels" value="1" />
653 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> 655 <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
654 </test> 656 </test>
655 <test> 657 <test>
656 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 658 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
657 <param name="license_agreement" value="true" /> 659 <param name="license_agreement" value="true" />
658 <param name="output_type" value="mz5" /> 660 <param name="output_type" value="mz5" />
659 <param name="mz_encoding" value="64" /> 661 <param name="mz_encoding" value="64" />
660 <param name="intensity_encoding" value="64" /> 662 <param name="intensity_encoding" value="64" />
661 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" /> 663 <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
662 </test> 664 </test>
663 <test> 665 <test>
664 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 666 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
665 <param name="license_agreement" value="true" /> 667 <param name="license_agreement" value="true" />
666 <param name="output_type" value="mzXML" /> 668 <param name="output_type" value="mzXML" />
667 <param name="mz_encoding" value="32" /> 669 <param name="mz_encoding" value="32" />
668 <param name="intensity_encoding" value="32" /> 670 <param name="intensity_encoding" value="32" />
669 <output name="output" file="small-zlib-32.mzXML" lines_diff="6" /> 671 <output name="output" file="small-zlib-32.mzXML" ftype="mzxml" lines_diff="6" />
670 </test> 672 </test>
671 <!-- TODO: how to test gzipped output? 673 <!-- TODO: how to test gzipped output?
672 <test> 674 <test>
673 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 675 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
674 <param name="output_type" value="mzXML" /> 676 <param name="output_type" value="mzXML" />
687 <param name="gzip_compression" value="true" /> 689 <param name="gzip_compression" value="true" />
688 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> 690 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
689 </test>--> 691 </test>-->
690 692
691 <test> 693 <test>
692 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 694 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
693 <param name="license_agreement" value="true" /> 695 <param name="license_agreement" value="true" />
694 <param name="output_type" value="mzML" /> 696 <param name="output_type" value="mzML" />
695 <param name="binary_compression" value="numpressLinearPic" /> 697 <param name="binary_compression" value="numpressLinearPic" />
696 <output name="output" file="small-numpressLP.mzML" lines_diff="114" /> 698 <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
697 </test> 699 </test>
698 700
699 <test> 701 <test>
700 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 702 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
701 <param name="license_agreement" value="true" /> 703 <param name="license_agreement" value="true" />
702 <param name="output_type" value="mzML" /> 704 <param name="output_type" value="mzML" />
703 <param name="binary_compression" value="numpressLinearSlof" /> 705 <param name="binary_compression" value="numpressLinearSlof" />
704 <output name="output" file="small-numpressLS.mzML" lines_diff="114" /> 706 <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
705 </test> 707 </test>
706 708
707 <test> 709 <test>
708 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 710 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
709 <param name="license_agreement" value="true" /> 711 <param name="license_agreement" value="true" />
710 <param name="output_type" value="mzML" /> 712 <param name="output_type" value="mzML" />
711 <param name="binary_compression" value="numpressLinear" /> 713 <param name="binary_compression" value="numpressLinear" />
712 <output name="output" file="small-numpressL.mzML" lines_diff="114" /> 714 <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
713 </test> 715 </test>
714 716
715 <test> 717 <test>
716 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 718 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
717 <param name="license_agreement" value="true" /> 719 <param name="license_agreement" value="true" />
718 <param name="output_type" value="mzML" /> 720 <param name="output_type" value="mzML" />
719 <param name="binary_compression" value="numpressPic" /> 721 <param name="binary_compression" value="numpressPic" />
720 <output name="output" file="small-numpressP.mzML" lines_diff="114" /> 722 <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
721 </test> 723 </test>
722 724
723 <test> 725 <test>
724 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 726 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
725 <param name="license_agreement" value="true" /> 727 <param name="license_agreement" value="true" />
726 <param name="output_type" value="mzML" /> 728 <param name="output_type" value="mzML" />
727 <param name="binary_compression" value="numpressSlof" /> 729 <param name="binary_compression" value="numpressSlof" />
728 <output name="output" file="small-numpressS.mzML" lines_diff="114" /> 730 <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
729 </test> 731 </test>
730 732
731 <test> 733 <test>
732 <param name="input" value="Rpal_01.mz5" /> 734 <param name="input" value="Rpal_01.mz5" ftype="mz5" />
733 <param name="license_agreement" value="true" /> 735 <param name="license_agreement" value="true" />
734 <param name="output_type" value="mzML" /> 736 <param name="output_type" value="mzML" />
735 <param name="binary_compression" value="numpressLinearPic" /> 737 <param name="binary_compression" value="numpressLinearPic" />
736 <param name="use_mzrefinement" value="true" /> 738 <param name="use_mzrefinement" value="true" />
737 <param name="input_ident" value="Rpal_01.pepXML" /> 739 <param name="input_ident" value="Rpal_01.pepXML" />
738 <param name="thresholdScore" value="mvh" /> 740 <param name="thresholdScore" value="mvh" />
739 <param name="thresholdValue" value="40-" /> 741 <param name="thresholdValue" value="40-" />
740 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> 742 <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
741 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> 743 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
742 </test> 744 </test>
743 745
744 <test> 746 <test>
745 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 747 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
746 <param name="license_agreement" value="true" /> 748 <param name="license_agreement" value="true" />
747 <param name="output_type" value="mzML" /> 749 <param name="output_type" value="mzML" />
748 <param name="binary_compression" value="numpressLinearPic" /> 750 <param name="binary_compression" value="numpressLinearPic" />
749 <param name="charge_state_calculation_method" value="predictor" /> 751 <param name="charge_state_calculation_method" value="predictor" />
750 <param name="predictor_overrideExistingCharge" value="true" /> 752 <param name="predictor_overrideExistingCharge" value="true" />
751 <param name="minMultipleCharge" value="2" /> 753 <param name="minMultipleCharge" value="2" />
752 <param name="maxMultipleCharge" value="5" /> 754 <param name="maxMultipleCharge" value="5" />
753 <param name="singleChargeFractionTIC" value="0.95" /> 755 <param name="singleChargeFractionTIC" value="0.95" />
754 <param name="maxKnownCharge" value="8" /> 756 <param name="maxKnownCharge" value="8" />
755 <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" /> 757 <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
756 </test> 758 </test>
757 <test> 759 <test>
758 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 760 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
759 <param name="license_agreement" value="true" /> 761 <param name="license_agreement" value="true" />
760 <param name="output_type" value="mzML" /> 762 <param name="output_type" value="mzML" />
761 <param name="binary_compression" value="numpressLinearPic" /> 763 <param name="binary_compression" value="numpressLinearPic" />
762 <param name="charge_state_calculation_method" value="turbocharger" /> 764 <param name="charge_state_calculation_method" value="turbocharger" />
763 <param name="minCharge" value="1" /> 765 <param name="minCharge" value="1" />
765 <param name="precursorsBefore" value="1" /> 767 <param name="precursorsBefore" value="1" />
766 <param name="precursorsAfter" value="1" /> 768 <param name="precursorsAfter" value="1" />
767 <param name="halfIsoWidth" value="1.5" /> 769 <param name="halfIsoWidth" value="1.5" />
768 <param name="defaultMinCharge" value="1" /> 770 <param name="defaultMinCharge" value="1" />
769 <param name="defaultMaxCharge" value="5" /> 771 <param name="defaultMaxCharge" value="5" />
770 <output name="output" file="small-turbocharger.mzML" lines_diff="114" /> 772 <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
771 </test> 773 </test>
772 <test> 774 <test>
773 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> 775 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
774 <param name="license_agreement" value="true" /> 776 <param name="license_agreement" value="true" />
775 <param name="output_type" value="mzML" /> 777 <param name="output_type" value="mzML" />
776 <param name="do_etd_filtering" value="true" /> 778 <param name="do_etd_filtering" value="true" />
777 <param name="remove_precursor" value="true" /> 779 <param name="remove_precursor" value="true" />
778 <param name="remove_charge_reduced" value="true" /> 780 <param name="remove_charge_reduced" value="true" />
779 <param name="remove_neutral_loss" value="false" /> 781 <param name="remove_neutral_loss" value="false" />
780 <param name="blanket_removal" value="false" /> 782 <param name="blanket_removal" value="false" />
781 <param name="matching_tolerance" value="50" /> 783 <param name="matching_tolerance" value="50" />
782 <param name="matching_tolerance_units" value="ppm" /> 784 <param name="matching_tolerance_units" value="ppm" />
783 <param name="binary_compression" value="numpressLinearPic" /> 785 <param name="binary_compression" value="numpressLinearPic" />
784 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" /> 786 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
785 </test> 787 </test>
786 <test> 788 <test>
787 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 789 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
788 <param name="license_agreement" value="true" /> 790 <param name="license_agreement" value="true" />
789 <param name="output_type" value="mzML" /> 791 <param name="output_type" value="mzML" />
790 <param name="thresholds_0|threshold_type" value="count" /> 792 <param name="thresholds_0|threshold_type" value="count" />
791 <param name="thresholds_0|value" value="100" /> 793 <param name="thresholds_0|value" value="100" />
792 <param name="thresholds_0|orientation" value="most-intense" /> 794 <param name="thresholds_0|orientation" value="most-intense" />
793 <param name="thresholds_1|threshold_type" value="absolute" /> 795 <param name="thresholds_1|threshold_type" value="absolute" />
794 <param name="thresholds_1|value" value="1" /> 796 <param name="thresholds_1|value" value="1" />
795 <param name="thresholds_1|orientation" value="most-intense" /> 797 <param name="thresholds_1|orientation" value="most-intense" />
796 <param name="binary_compression" value="numpressLinearPic" /> 798 <param name="binary_compression" value="numpressLinearPic" />
797 <output name="output" file="small-threshold.mzML" lines_diff="114" /> 799 <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
798 </test> 800 </test>
799 <test> 801 <test>
800 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 802 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
801 <param name="license_agreement" value="true" /> 803 <param name="license_agreement" value="true" />
802 <param name="output_type" value="mzML" /> 804 <param name="output_type" value="mzML" />
803 <param name="do_mzwindow_filter" value="true" /> 805 <param name="do_mzwindow_filter" value="true" />
804 <param name="mz_window_from" value="420" /> 806 <param name="mz_window_from" value="420" />
805 <param name="mz_window_to" value="840" /> 807 <param name="mz_window_to" value="840" />
806 <param name="binary_compression" value="numpressLinearPic" /> 808 <param name="binary_compression" value="numpressLinearPic" />
807 <output name="output" file="small-mzWindow.mzML" lines_diff="114" /> 809 <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
808 </test> 810 </test>
809 <test> 811 <test>
810 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 812 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
811 <param name="license_agreement" value="true" /> 813 <param name="license_agreement" value="true" />
812 <param name="output_type" value="mzML" /> 814 <param name="output_type" value="mzML" />
813 <param name="denoise" value="true" /> 815 <param name="denoise" value="true" />
814 <param name="num_peaks" value="10" /> 816 <param name="num_peaks" value="10" />
815 <param name="window_width" value="40" /> 817 <param name="window_width" value="40" />
816 <param name="relax" value="false" /> 818 <param name="relax" value="false" />
817 <param name="binary_compression" value="numpressLinearPic" /> 819 <param name="binary_compression" value="numpressLinearPic" />
818 <output name="output" file="small-denoise.mzML" lines_diff="114" /> 820 <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
819 </test> 821 </test>
820 <test> 822 <test>
821 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 823 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
822 <param name="license_agreement" value="true" /> 824 <param name="license_agreement" value="true" />
823 <param name="output_type" value="mzML" /> 825 <param name="output_type" value="mzML" />
824 <param name="ms2deisotope" value="true" /> 826 <param name="ms2deisotope" value="true" />
825 <param name="binary_compression" value="numpressLinearPic" /> 827 <param name="binary_compression" value="numpressLinearPic" />
826 <output name="output" file="small-deisotope.mzML" lines_diff="114" /> 828 <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
827 </test> 829 </test>
828 <test> 830 <test>
829 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 831 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
830 <param name="license_agreement" value="true" /> 832 <param name="license_agreement" value="true" />
831 <param name="output_type" value="mzML" /> 833 <param name="output_type" value="mzML" />
832 <param name="activation" value="CID" /> 834 <param name="activation" value="CID" />
833 <param name="binary_compression" value="numpressLinearPic" /> 835 <param name="binary_compression" value="numpressLinearPic" />
834 <output name="output" file="small-activation.mzML" lines_diff="114" /> 836 <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
835 </test> 837 </test>
836 <test> 838 <test>
837 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 839 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
838 <param name="license_agreement" value="true" /> 840 <param name="license_agreement" value="true" />
839 <param name="output_type" value="mzML" /> 841 <param name="output_type" value="mzML" />
840 <param name="indices_0|from" value="2" /> 842 <param name="indices_0|from" value="2" />
841 <param name="indices_0|to" value="4" /> 843 <param name="indices_0|to" value="4" />
842 <param name="indices_1|from" value="10" /> 844 <param name="indices_1|from" value="10" />
843 <param name="indices_1|to" value="10" /> 845 <param name="indices_1|to" value="10" />
844 <param name="indices_2|from" value="13" /> 846 <param name="indices_2|from" value="13" />
845 <param name="indices_2|to" value="15" /> 847 <param name="indices_2|to" value="15" />
846 <param name="binary_compression" value="numpressLinearPic" /> 848 <param name="binary_compression" value="numpressLinearPic" />
847 <output name="output" file="small-index-filter.mzML" lines_diff="32" /> 849 <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
848 </test> 850 </test>
849 <test> 851 <test>
850 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 852 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
851 <param name="license_agreement" value="true" /> 853 <param name="license_agreement" value="true" />
852 <param name="output_type" value="mzML" /> 854 <param name="output_type" value="mzML" />
853 <param name="strip_it" value="true" /> 855 <param name="strip_it" value="true" />
854 <param name="binary_compression" value="numpressLinearPic" /> 856 <param name="binary_compression" value="numpressLinearPic" />
855 <output name="output" file="small-strip-it.mzML" lines_diff="100" /> 857 <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
856 </test> 858 </test>
857 <test> 859 <test>
858 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 860 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
859 <param name="license_agreement" value="true" /> 861 <param name="license_agreement" value="true" />
860 <param name="output_type" value="mzML" /> 862 <param name="output_type" value="mzML" />
861 <param name="do_ms_level_filter" value="true" /> 863 <param name="do_ms_level_filter" value="true" />
862 <param name="ms_level_from" value="2" /> 864 <param name="ms_level_from" value="2" />
863 <param name="ms_level_to" value="2" /> 865 <param name="ms_level_to" value="2" />
864 <param name="binary_compression" value="numpressLinearPic" /> 866 <param name="binary_compression" value="numpressLinearPic" />
865 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" /> 867 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
866 </test> 868 </test>
867 <test> 869 <test>
868 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 870 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
869 <param name="license_agreement" value="true" /> 871 <param name="license_agreement" value="true" />
870 <param name="output_type" value="mzML" /> 872 <param name="output_type" value="mzML" />
871 <param name="polarity" value="positive" /> 873 <param name="polarity" value="positive" />
872 <param name="binary_compression" value="numpressLinearPic" /> 874 <param name="binary_compression" value="numpressLinearPic" />
873 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" /> 875 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
874 </test> 876 </test>
875 <test> 877 <test>
876 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 878 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
877 <param name="license_agreement" value="true" /> 879 <param name="license_agreement" value="true" />
878 <param name="output_type" value="mzML" /> 880 <param name="output_type" value="mzML" />
879 <param name="analyzer" value="IT" /> 881 <param name="analyzer" value="IT" />
880 <param name="binary_compression" value="numpressLinearPic" /> 882 <param name="binary_compression" value="numpressLinearPic" />
881 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" /> 883 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
882 </test> 884 </test>
883 <test> 885 <test>
884 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 886 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
885 <param name="license_agreement" value="true" /> 887 <param name="license_agreement" value="true" />
886 <param name="output_type" value="mzML" /> 888 <param name="output_type" value="mzML" />
887 <param name="scan_numbers_0|from" value="3" /> 889 <param name="scan_numbers_0|from" value="3" />
888 <param name="scan_numbers_0|to" value="5" /> 890 <param name="scan_numbers_0|to" value="5" />
889 <param name="scan_numbers_1|from" value="11" /> 891 <param name="scan_numbers_1|from" value="11" />
890 <param name="scan_numbers_1|to" value="11" /> 892 <param name="scan_numbers_1|to" value="11" />
891 <param name="scan_numbers_2|from" value="14" /> 893 <param name="scan_numbers_2|from" value="14" />
892 <param name="scan_numbers_2|to" value="16" /> 894 <param name="scan_numbers_2|to" value="16" />
893 <param name="binary_compression" value="numpressLinearPic" /> 895 <param name="binary_compression" value="numpressLinearPic" />
894 <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above --> 896 <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above -->
895 </test> 897 </test>
896 <!--<test> 898 <!--<test>
897 <param name="input" value="small.mzML" /> 899 <param name="input" value="small.mzML" />
898 <param name="output_type" value="mzML" /> 900 <param name="output_type" value="mzML" />
899 <param name="binary_compression" value="numpressLinearPic" /> 901 <param name="binary_compression" value="numpressLinearPic" />