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comparison maxquant.xml @ 21:8934bc76bb52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:02:17 +0000
parents 163452d1e255
children 9c52362ae7bb
comparison
equal deleted inserted replaced
20:837224ad1694 21:8934bc76bb52
1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <macros> 2 <macros>
3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
5 <filter>'@NAME@' in output_opts['output']</filter>
6 </data>
7 </xml>
8 <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
9 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
10 <filter>'@NAME@' in output_opts['output']</filter>
11 </data>
12 </xml>
13 <import>macros.xml</import> 3 <import>macros.xml</import>
14 </macros> 4 </macros>
15 <expand macro="requirements"/> 5 <expand macro="requirements"/>
16 <expand macro="required_files"/> 6 <expand macro="required_files"/>
17 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
18 ## this is needed to avoid dotnet from crashing, in a newer dotnet version we can remove that 8 ## this is needed to avoid dotnet from crashing, in a newer dotnet version we can remove that
19 export COMPlus_EnableDiagnostics=0 && 9 export COMPlus_EnableDiagnostics=0 &&
20 #import re 10 #import re
21 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr 11 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr
22
23 ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0)
24 ## Should be removed as soon as MQ is updated with a fixed version
25 &&
26 sed -i -E 's:(maxQuantVersion>)1.6.5.0(<):\1'1.6.17.0'\2:' mqpar.xml
27 ## ==============================================================================================
28 12
29 #if 'config' in $output_opts.output: 13 #if 'config' in $output_opts.output:
30 && 14 &&
31 cp '$mq_conf' '$config' 15 cp '$mq_conf' '$config'
32 #end if 16 #end if
68 #if 'output_all' in $output_opts.output: 52 #if 'output_all' in $output_opts.output:
69 && 53 &&
70 tar -zcf '$output_all' ./combined/txt 54 tar -zcf '$output_all' ./combined/txt
71 #end if 55 #end if
72 56
73 #if $qc.do_it: 57 #if $qc.do_it == 'true':
74 && 58 &&
75 Rscript '$qr' '$qr_yaml' 59 Rscript '$qr' '$qr_yaml'
76 #if 'log' in $output_opts.output: 60 #if 'log' in $output_opts.output:
77 >> '$log' 2>&1 61 >> '$log' 2>&1
78 #end if 62 #end if
511 <option value="0">None</option> 495 <option value="0">None</option>
512 <option value="1" selected="true">Classic</option> 496 <option value="1" selected="true">Classic</option>
513 </param> 497 </param>
514 </when> 498 </when>
515 <when value="reporter_ion_ms2"> 499 <when value="reporter_ion_ms2">
516 <conditional name="iso_labels"> 500 <expand macro="reporter_ion_macro"/>
517 <param name="labeling" type="select" label="isobaric labeling"
518 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
519 <option value="custom">custom</option>
520 <option value="tmt2plex">TMT2plex</option>
521 <option value="tmt6plex">TMT6plex</option>
522 <option value="tmt8plex">TMT8plex</option>
523 <option value="tmt10plex">TMT10plex</option>
524 <option value="tmt11plex">TMT11plex</option>
525 <option value="tmtpro16plex">TMTpro16plex</option>
526 <option value="tmtpro18plex">TMTpro18plex</option>
527 <option value="itraq4plex">iTRAQ4plex</option>
528 <option value="itraq8plex">iTRAQ8plex</option>
529 <option value="iodotmt6plex">iodoTMT6plex</option>
530 </param>
531 <when value="tmt2plex"/>
532 <when value="tmt6plex"/>
533 <when value="tmt8plex"/>
534 <when value="tmt10plex"/>
535 <when value="tmt11plex"/>
536 <when value="tmtpro16plex"/>
537 <when value="tmtpro18plex"/>
538 <when value="itraq4plex"/>
539 <when value="itraq8plex"/>
540 <when value="iodotmt6plex"/>
541 <when value="custom">
542 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
543 <param name="internallabel" type="select" label="internal label" help="contains Lys">
544 <expand macro="iso_labels"/>
545 </param>
546 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
547 <option value="">None</option>
548 <expand macro="iso_labels"/>
549 </param>
550 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
551 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
552 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
553 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
554 <param type="boolean" name="tmtlike" checked="false"
555 label="TMT-like"
556 truevalue="True" falsevalue="False"/>
557 </repeat>
558 </when>
559 </conditional>
560 <conditional name="filter_by_pif">
561 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
562 truevalue="True" falsevalue="False"
563 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
564 <when value="True">
565 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
566 max="1"
567 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
568 </when>
569 <when value="False"/>
570 </conditional>
571 </when> 501 </when>
572 <when value="reporter_ion_ms3"> 502 <when value="reporter_ion_ms3">
573 <conditional name="iso_labels"> 503 <expand macro="reporter_ion_macro"/>
574 <param name="labeling" type="select" label="isobaric labeling"
575 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
576 <option value="custom">custom</option>
577 <option value="tmt2plex">TMT2plex</option>
578 <option value="tmt6plex">TMT6plex</option>
579 <option value="tmt8plex">TMT8plex</option>
580 <option value="tmt10plex">TMT10plex</option>
581 <option value="tmt11plex">TMT11plex</option>
582 <option value="tmtpro16plex">TMTpro16plex</option>
583 <option value="tmtpro18plex">TMTpro18plex</option>
584 <option value="itraq4plex">iTRAQ4plex</option>
585 <option value="itraq8plex">iTRAQ8plex</option>
586 <option value="iodotmt6plex">iodoTMT6plex</option>
587 </param>
588 <when value="tmt2plex"/>
589 <when value="tmt6plex"/>
590 <when value="tmt8plex"/>
591 <when value="tmt10plex"/>
592 <when value="tmt11plex"/>
593 <when value="tmtpro16plex"/>
594 <when value="tmtpro18plex"/>
595 <when value="itraq4plex"/>
596 <when value="itraq8plex"/>
597 <when value="iodotmt6plex"/>
598 <when value="custom">
599 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
600 <param name="internallabel" type="select" label="internal label" help="contains Lys">
601 <expand macro="iso_labels"/>
602 </param>
603 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
604 <option value="">None</option>
605 <expand macro="iso_labels"/>
606 </param>
607 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
608 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
609 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
610 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
611 <param type="boolean" name="tmtlike" checked="false"
612 label="TMT-like"
613 truevalue="True" falsevalue="False"/>
614 </repeat>
615 </when>
616 </conditional>
617 <conditional name="filter_by_pif">
618 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
619 truevalue="True" falsevalue="False"
620 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
621 <when value="True">
622 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
623 max="1"
624 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
625 </when>
626 <when value="False"/>
627 </conditional>
628 </when> 504 </when>
629 </conditional> 505 </conditional>
630 </repeat> 506 </repeat>
631 507
632 <expand macro="ptxqc-opts"/> 508 <expand macro="ptxqc-opts"/>
662 538
663 <expand macro="outputs"/> 539 <expand macro="outputs"/>
664 540
665 <tests> 541 <tests>
666 <!-- functional test with small mzXML file, no quantitation methods --> 542 <!-- functional test with small mzXML file, no quantitation methods -->
667 <!-- Disable this test when initally testing as it takes avery long tome to run --> 543 <test expect_num_outputs="14">
668 <test expect_num_outputs="15">
669 <param name="ftype" value=".mzxml" /> 544 <param name="ftype" value=".mzxml" />
670 <param name="fasta_files" value="bsa.fasta" /> 545 <param name="fasta_files" value="bsa.fasta" />
671 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 546 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
672 <param name="description_parse_rule" value="&gt;(.*)" /> 547 <param name="description_parse_rule" value="&gt;(.*)" />
673 <repeat name="paramGroups"> 548 <repeat name="paramGroups">
675 <param name="maxMissedCleavages" value="1"/> 550 <param name="maxMissedCleavages" value="1"/>
676 <param name="fixedModifications" value="Carbamidomethyl (C)" /> 551 <param name="fixedModifications" value="Carbamidomethyl (C)" />
677 <param name="variableModifications" value="Oxidation (M)" /> 552 <param name="variableModifications" value="Oxidation (M)" />
678 <param name="enzymes" value="Trypsin/P" /> 553 <param name="enzymes" value="Trypsin/P" />
679 </repeat> 554 </repeat>
680 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" /> 555 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" />
681 <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/> 556 <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/>
682 <output name="evidence" file="01/combined/txt/evidence.txt" /> 557 <output name="evidence">
558 <assert_contents>
559 <has_n_lines n="7"/>
560 <has_n_columns n="58"/>
561 </assert_contents>
562 </output>
683 <output name="msms" file="01/combined/txt/msms.txt" /> 563 <output name="msms" file="01/combined/txt/msms.txt" />
684 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/> 564 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34" ftype="mztab"/>
685 <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="2"/> 565 <output name="allPeptides">
686 <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/> 566 <assert_contents>
687 <output name="mzRange" file="01/combined/txt/mzRange.txt" /> 567 <has_n_lines n="159"/>
568 <has_n_columns n="35"/>
569 </assert_contents>
570 </output>
571 <output name="msmsScans">
572 <assert_contents>
573 <has_n_lines n="82"/>
574 <has_n_columns n="46"/>
575 </assert_contents>
576 </output>
577 <output name="mzRange">
578 <assert_contents>
579 <has_n_lines n="1881"/>
580 <has_n_columns n="12"/>
581 </assert_contents>
582 </output>
688 <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/> 583 <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/>
689 <output name="peptides" file="01/combined/txt/peptides.txt" /> 584 <output name="peptides">
690 <output name="peptideSection" file="01/combined/txt/peptideSection.txt" /> 585 <assert_contents>
691 <output name="proteinGroups" file="01/combined/txt/proteinGroups.txt" /> 586 <has_n_lines n="7"/>
692 <output name="summary" file="01/combined/txt/summary.txt" /> 587 <has_n_columns n="57"/>
693 <output name="modificationSpecificPeptides" file="01/combined/txt/modificationSpecificPeptides.txt" /> 588 </assert_contents>
589 </output>
590 <output name="proteinGroups">
591 <assert_contents>
592 <has_n_lines n="7"/>
593 <has_n_columns n="39"/>
594 </assert_contents>
595 </output>
596 <output name="summary">
597 <assert_contents>
598 <has_n_lines n="3"/>
599 <has_n_columns n="51"/>
600 </assert_contents>
601 </output>
602 <output name="modificationSpecificPeptides">
603 <assert_contents>
604 <has_n_lines n="7"/>
605 <has_n_columns n="32"/>
606 </assert_contents>
607 </output>
694 <output name="config" file="01/config.yml" lines_diff="2"/> 608 <output name="config" file="01/config.yml" lines_diff="2"/>
695 </test> 609 </test>
696 <!-- reporter ion ms2 + multiple param groups, testing yaml conf file and mqpar.xml only --> 610 <!-- 2 reporter ion ms2 + multiple param groups, testing yaml conf file and mqpar.xml only -->
697 <test expect_num_outputs="3"> 611 <test expect_num_outputs="3">
698 <param name="ftype" value=".mzxml" /> 612 <param name="ftype" value=".mzxml" />
699 <param name="fasta_files" value="bsa.fasta" /> 613 <param name="fasta_files" value="bsa.fasta" />
700 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 614 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
701 <param name="description_parse_rule" value="&gt;(.*)" /> 615 <param name="description_parse_rule" value="&gt;(.*)" />
757 </conditional> 671 </conditional>
758 </repeat> 672 </repeat>
759 <param name="dry_run" value="True" /> 673 <param name="dry_run" value="True" />
760 <param name="output" value="config,mqpar,mzTab" /> 674 <param name="output" value="config,mqpar,mzTab" />
761 <output name="config" file="02/config.yml" lines_diff="7" /> 675 <output name="config" file="02/config.yml" lines_diff="7" />
762 <!-- high difference due to unconsistant xml formatting in MQ --> 676 <output name="mqpar" file="02/mqpar.xml" lines_diff="8" />
763 <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />
764 </test> 677 </test>
765 <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only --> 678 <!-- 3 reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only -->
766 <test expect_num_outputs="3"> 679 <test expect_num_outputs="3">
767 <param name="ftype" value=".mzxml" /> 680 <param name="ftype" value=".mzxml" />
768 <param name="fasta_files" value="bsa.fasta" /> 681 <param name="fasta_files" value="bsa.fasta" />
769 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 682 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
770 <param name="description_parse_rule" value="&gt;(.*)" /> 683 <param name="description_parse_rule" value="&gt;(.*)" />
830 <output name="config" file="06/config.yml" lines_diff="7"> 743 <output name="config" file="06/config.yml" lines_diff="7">
831 <assert_contents> 744 <assert_contents>
832 <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" /> 745 <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" />
833 </assert_contents> 746 </assert_contents>
834 </output> 747 </output>
835 <output name="mqpar" file="06/mqpar.xml" lines_diff="6"> 748 <output name="mqpar" file="06/mqpar.xml" lines_diff="8">
836 <assert_contents> 749 <assert_contents>
837 <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." /> 750 <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." />
838 </assert_contents> 751 </assert_contents>
839 </output> 752 </output>
840 </test> 753 </test>
841 <!-- lfq, testing yaml conf file and mqpar.xml only --> 754 <!-- 4 lfq, testing yaml conf file and mqpar.xml only -->
842 <test expect_num_outputs="2"> 755 <test expect_num_outputs="2">
843 <param name="ftype" value=".mzxml" /> 756 <param name="ftype" value=".mzxml" />
844 <param name="fasta_files" value="bsa.fasta" /> 757 <param name="fasta_files" value="bsa.fasta" />
845 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" /> 758 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
846 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" /> 759 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
856 </conditional> 769 </conditional>
857 </repeat> 770 </repeat>
858 <param name="dry_run" value="True" /> 771 <param name="dry_run" value="True" />
859 <param name="output" value="config,mqpar" /> 772 <param name="output" value="config,mqpar" />
860 <output name="config" file="03/config.yml" lines_diff="2" /> 773 <output name="config" file="03/config.yml" lines_diff="2" />
861 <output name="mqpar" file="03/mqpar.xml" lines_diff="10" /> 774 <output name="mqpar" file="03/mqpar.xml" lines_diff="6" />
862 </test> 775 </test>
863 <!-- Test for MBR --> 776 <!-- 5 Test for MBR -->
864 <test expect_num_outputs="2"> 777 <test expect_num_outputs="2">
865 <param name="ftype" value=".mzxml" /> 778 <param name="ftype" value=".mzxml" />
866 <param name="fasta_files" value="bsa.fasta" /> 779 <param name="fasta_files" value="bsa.fasta" />
867 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" /> 780 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
868 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" /> 781 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
883 <output name="config" file="05/config.yml" lines_diff="2"> 796 <output name="config" file="05/config.yml" lines_diff="2">
884 <assert_contents> 797 <assert_contents>
885 <has_text_matching expression="matchBetweenRuns\: True" /> 798 <has_text_matching expression="matchBetweenRuns\: True" />
886 </assert_contents> 799 </assert_contents>
887 </output> 800 </output>
888 <output name="mqpar" file="05/mqpar.xml" lines_diff="4"> 801 <output name="mqpar" file="05/mqpar.xml" lines_diff="6">
889 <assert_contents> 802 <assert_contents>
890 <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." /> 803 <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." />
891 </assert_contents> 804 </assert_contents>
892 </output> 805 </output>
893 </test> 806 </test>
894 <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only --> 807 <!-- 6 silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->
895 <test expect_num_outputs="2"> 808 <test expect_num_outputs="2">
896 <param name="ftype" value=".mzxml" /> 809 <param name="ftype" value=".mzxml" />
897 <param name="fasta_files" value="bsa.fasta" /> 810 <param name="fasta_files" value="bsa.fasta" />
898 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 811 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
899 <param name="description_parse_rule" value="&gt;(.*)" /> 812 <param name="description_parse_rule" value="&gt;(.*)" />
912 <param name="dry_run" value="True" /> 825 <param name="dry_run" value="True" />
913 <param name="output" value="config,mqpar" /> 826 <param name="output" value="config,mqpar" />
914 <output name="config" file="04/config.yml" lines_diff="2" /> 827 <output name="config" file="04/config.yml" lines_diff="2" />
915 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" /> 828 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />
916 </test> 829 </test>
917 <!-- PTXQC Test --> 830 <!-- 7 PTXQC Test -->
918 <test expect_num_outputs="3"> 831 <test expect_num_outputs="3">
919 <param name="ftype" value=".mzxml" /> 832 <param name="ftype" value=".mzxml" />
920 <param name="fasta_files" value="tmt_data.fasta" /> 833 <param name="fasta_files" value="tmt_data.fasta" />
921 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 834 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
922 <param name="description_parse_rule" value="&gt;(.*)" /> 835 <param name="description_parse_rule" value="&gt;(.*)" />
929 <conditional name="iso_labels"> 842 <conditional name="iso_labels">
930 <param name="labeling" value="tmt10plex" /> 843 <param name="labeling" value="tmt10plex" />
931 </conditional> 844 </conditional>
932 </conditional> 845 </conditional>
933 </repeat> 846 </repeat>
934 <param name="do_it" value="True" /> 847 <param name="do_it" value="true" />
935 <param name="output" value="config,mqpar" /> 848 <param name="output" value="config,mqpar" />
936 <output name="config" file="07/config.yml" lines_diff="2" /> 849 <output name="config" file="07/config.yml" lines_diff="2" />
937 <!-- high difference due to unconsistant xml formatting in MQ --> 850 <!-- high difference due to unconsistant xml formatting in MQ -->
938 <output name="mqpar" file="07/mqpar.xml" lines_diff="4" /> 851 <output name="mqpar" file="07/mqpar.xml" lines_diff="6" />
939 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" /> 852 <output name="ptxqc_report">
853 <assert_contents>
854 <has_line line="%PDF-1.4"/>
855 <!-- was 50k for older versions, now 88K (for 30-pages) -->
856 <has_size min="40K" max="100K"/>
857 </assert_contents>
858 </output>
940 </test> 859 </test>
941 <!-- TMTpro16plex test --> 860 <!-- 8 TMTpro16plex test -->
942 <test expect_num_outputs="3"> 861 <test expect_num_outputs="3">
943 <param name="ftype" value=".mzxml" /> 862 <param name="ftype" value=".mzxml" />
944 <param name="fasta_files" value="tmt_data_16.fasta" /> 863 <param name="fasta_files" value="tmt_data_16.fasta" />
945 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 864 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
946 <param name="description_parse_rule" value="&gt;(.*)" /> 865 <param name="description_parse_rule" value="&gt;(.*)" />
953 <conditional name="iso_labels"> 872 <conditional name="iso_labels">
954 <param name="labeling" value="tmtpro16plex" /> 873 <param name="labeling" value="tmtpro16plex" />
955 </conditional> 874 </conditional>
956 </conditional> 875 </conditional>
957 </repeat> 876 </repeat>
958 <param name="do_it" value="False" /> 877 <param name="do_it" value="false" />
959 <param name="output" value="config,mqpar,proteinGroups" /> 878 <param name="output" value="config,mqpar,proteinGroups" />
960 <output name="config" file="08/config.yml" lines_diff="2" /> 879 <output name="config" file="08/config.yml" lines_diff="2" />
961 <!-- high difference due to unconsistant xml formatting in MQ --> 880 <!-- high difference due to unconsistant xml formatting in MQ -->
962 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" /> 881 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" />
963 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" /> 882 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />
964 </test> 883 </test>
965 <!-- TMTpro18plex test --> 884 <!-- 9 TMTpro18plex test -->
966 <test expect_num_outputs="2"> 885 <test expect_num_outputs="2">
967 <param name="ftype" value=".mzxml" /> 886 <param name="ftype" value=".mzxml" />
968 <param name="fasta_files" value="tmt_data_18.fasta" /> 887 <param name="fasta_files" value="tmt_data_18.fasta" />
969 <param name="identifier_parse_rule" value="&gt;([^\s]*)" /> 888 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
970 <param name="description_parse_rule" value="&gt;(.*)" /> 889 <param name="description_parse_rule" value="&gt;(.*)" />
977 <conditional name="iso_labels"> 896 <conditional name="iso_labels">
978 <param name="labeling" value="tmtpro18plex" /> 897 <param name="labeling" value="tmtpro18plex" />
979 </conditional> 898 </conditional>
980 </conditional> 899 </conditional>
981 </repeat> 900 </repeat>
982 <param name="do_it" value="False" /> 901 <param name="do_it" value="false" />
983 <param name="output" value="msmsScans" /> 902 <param name="output" value="msmsScans" />
984 <output name="msmsScans" file="09/combined/txt/msmsScans.txt"> 903 <output name="msmsScans" file="09/combined/txt/msmsScans.txt">
985 <assert_contents> 904 <assert_contents>
986 <has_text text="GANDSMMM" /> 905 <has_text text="GANDSMMM" />
987 </assert_contents> 906 </assert_contents>
988 </output> 907 </output>
989 </test> 908 </test>
990 <!-- Thermo RAW file test --> 909 <!-- 10 Thermo RAW file test -->
991 <test expect_num_outputs="2"> 910 <test expect_num_outputs="2">
992 <param name="ftype" value=".thermo.raw" /> 911 <param name="ftype" value=".thermo.raw" />
993 <param name="fasta_files" value="bsa.fasta" /> 912 <param name="fasta_files" value="bsa.fasta" />
994 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" /> 913 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
995 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" /> 914 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />