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comparison jbrowse2.xml @ 63:ac00dcfb5d1d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
author fubar
date Thu, 28 Mar 2024 07:46:04 +0000
parents ab0d6782a95f
children 497fd2d27aa2
comparison
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62:ab0d6782a95f 63:ac00dcfb5d1d
539 <param name="uglyTestingHack" value="enabled" /> 539 <param name="uglyTestingHack" value="enabled" />
540 <output name="output"> 540 <output name="output">
541 <assert_contents> 541 <assert_contents>
542 <has_text text="genome path="></has_text> 542 <has_text text="genome path="></has_text>
543 <has_text text="label="></has_text> 543 <has_text text="label="></has_text>
544 <has_text text="format="></has_text> 544 <has_text text="useuri="></has_text>
545 <has_text text="metadata"></has_text> 545 <has_text text="metadata"></has_text>
546 </assert_contents> 546 </assert_contents>
547 </output> 547 </output>
548 </test> 548 </test>
549 <test> 549 <test>
574 <has_text text="label="></has_text> 574 <has_text text="label="></has_text>
575 <has_text text="format="></has_text> 575 <has_text text="format="></has_text>
576 <has_text text="metadata"></has_text> 576 <has_text text="metadata"></has_text>
577 <has_text text="useuri="></has_text> 577 <has_text text="useuri="></has_text>
578 <has_text text="trackFile path="></has_text> 578 <has_text text="trackFile path="></has_text>
579 <has_text text="ext=&quot;bed&quot; label=&quot;test-3.bed&quot;"></has_text> 579 <has_text text="ext=&quot;vcf&quot; label=&quot;merlin.vcf&quot;"></has_text>
580 </assert_contents> 580 </assert_contents>
581 </output> 581 </output>
582 </test> 582 </test>
583 <test> 583 <test>
584 <repeat name="assemblies"> 584 <repeat name="assemblies">
586 <param name="genome_type_select" value="history"/> 586 <param name="genome_type_select" value="history"/>
587 <param name="genome" value="merlin.fa"/> 587 <param name="genome" value="merlin.fa"/>
588 <param name="genome.ext" value="fasta"/> 588 <param name="genome.ext" value="fasta"/>
589 <param name="genome.name" value="Merlin"/> 589 <param name="genome.name" value="Merlin"/>
590 </conditional> 590 </conditional>
591 <repeat name="track_groups"> 591 <repeat name="track_groups">
592 <param name="category" value="Default" /> 592 <param name="category" value="Default" />
593 <repeat name="data_tracks"> 593 <repeat name="data_tracks">
594 <conditional name="data_format"> 594 <conditional name="data_format">
595 <param name="data_format_select" value="gff"/> 595 <param name="data_format_select" value="gff"/>
596 <conditional name="useuri"> 596 <conditional name="useuri">
609 <param name="color_select" value="automatic"/> 609 <param name="color_select" value="automatic"/>
610 </conditional> 610 </conditional>
611 </section> 611 </section>
612 </repeat> 612 </repeat>
613 </repeat> 613 </repeat>
614 </repeat> 614 <repeat name="track_groups">
615
616 <repeat name="track_groups">
617 <param name="category" value="Ignore Scale" /> 615 <param name="category" value="Ignore Scale" />
618 <repeat name="data_tracks"> 616 <repeat name="data_tracks">
619 <conditional name="data_format"> 617 <conditional name="data_format">
620 <param name="data_format_select" value="gff"/> 618 <param name="data_format_select" value="gff"/>
621 <conditional name="useuri"> 619 <conditional name="useuri">
622 <param name="insource" value="history"/> 620 <param name="insource" value="history"/>
623 <param name="annotation" value="gff3/1.gff"/> 621 <param name="annotation" value="gff3/1.gff"/>
633 <param name="style_color" value="#ff00ff"/> 631 <param name="style_color" value="#ff00ff"/>
634 </conditional> 632 </conditional>
635 </conditional> 633 </conditional>
636 </section> 634 </section>
637 </conditional> 635 </conditional>
636 </repeat>
638 </repeat> 637 </repeat>
639 </repeat> 638 <repeat name="track_groups">
640
641 <repeat name="track_groups">
642 <param name="category" value="Scaled Colour" /> 639 <param name="category" value="Scaled Colour" />
643 <repeat name="data_tracks"> 640 <repeat name="data_tracks">
644 <conditional name="data_format"> 641 <conditional name="data_format">
645 <param name="data_format_select" value="gff"/> 642 <param name="data_format_select" value="gff"/>
646 <conditional name="useuri"> 643 <conditional name="useuri">
647 <param name="insource" value= "history"/> 644 <param name="insource" value= "history"/>
648 <param name="annotation" value="gff3/C.gff"/> 645 <param name="annotation" value="gff3/C.gff"/>
649 </conditional> 646 </conditional>
650 <conditional name="match_part"> 647 <conditional name="match_part">
651 <param name="match_part_select" value="false"/> 648 <param name="match_part_select" value="false"/>
652 </conditional> 649 </conditional>
653 <section name="jbcolor_scale"> 650 <section name="jbcolor_scale">
654 <conditional name="color_score"> 651 <conditional name="color_score">
655 <param name="color_score_select" value="score"/> 652 <param name="color_score_select" value="score"/>
656 <param name="score_scaling" value="linear"/> 653 <param name="score_scaling" value="linear"/>
657 <conditional name="score_scales"> 654 <conditional name="score_scales">
658 <param name="scale_select" value="automatic"/> 655 <param name="scale_select" value="automatic"/>
659 </conditional> 656 </conditional>
660 <conditional name="color_scheme"> 657 <conditional name="color_scheme">
661 <param name="score_scheme" value="opacity"/> 658 <param name="score_scheme" value="opacity"/>
662 <conditional name="color"> 659 <conditional name="color">
663 <param name="color_select" value="automatic"/> 660 <param name="color_select" value="automatic"/>
661 </conditional>
664 </conditional> 662 </conditional>
665 </conditional> 663 </conditional>
666 </conditional> 664 </section>
667 </section> 665 </conditional>
668 </conditional> 666 </repeat>
669 </repeat> 667 <repeat name="data_tracks">
670 <repeat name="data_tracks"> 668 <conditional name="data_format">
671 <conditional name="data_format"> 669 <param name="data_format_select" value="gff"/>
672 <param name="data_format_select" value="gff"/> 670 <conditional name="useuri">
673 <conditional name="useuri"> 671 <param name="annotation" value="gff3/B.gff"/>
674 <param name="annotation" value="gff3/B.gff"/> 672 <param name="insource" value= "history"/>
675 <param name="insource" value= "history"/> 673 </conditional>
676 </conditional> 674 <conditional name="match_part">
677 <conditional name="match_part"> 675 <param name="match_part_select" value="false"/>
678 <param name="match_part_select" value="false"/> 676 </conditional>
679 </conditional> 677 <section name="jbcolor_scale">
680 <section name="jbcolor_scale"> 678 <conditional name="color_score">
681 <conditional name="color_score"> 679 <param name="color_score_select" value="score"/>
682 <param name="color_score_select" value="score"/> 680 <param name="score_scaling" value="linear"/>
683 <param name="score_scaling" value="linear"/> 681 <conditional name="score_scales">
684 <conditional name="score_scales"> 682 <param name="scale_select" value="automatic"/>
685 <param name="scale_select" value="automatic"/> 683 </conditional>
686 </conditional> 684 <conditional name="color_scheme">
687 <conditional name="color_scheme"> 685 <param name="score_scheme" value="opacity"/>
688 <param name="score_scheme" value="opacity"/> 686 <conditional name="color">
689 <conditional name="color"> 687 <param name="color_select" value="manual"/>
690 <param name="color_select" value="manual"/> 688 <param name="style_color" value="#0000ff"/>
691 <param name="style_color" value="#0000ff"/> 689 </conditional>
692 </conditional> 690 </conditional>
693 </conditional> 691 </conditional>
694 </conditional> 692 </section>
695 </section> 693 </conditional>
696 </conditional> 694 </repeat>
697 </repeat> 695 <repeat name="data_tracks">
698 <repeat name="data_tracks"> 696 <conditional name="data_format">
699 <conditional name="data_format"> 697 <param name="data_format_select" value="gff"/>
700 <param name="data_format_select" value="gff"/> 698 <conditional name="useuri">
701 <conditional name="useuri"> 699 <param name="annotation" value="gff3/A.gff"/>
702 <param name="annotation" value="gff3/A.gff"/> 700 <param name="insource" value= "history"/>
703 <param name="insource" value= "history"/> 701 </conditional>
704 </conditional> 702 <conditional name="match_part">
705 <conditional name="match_part"> 703 <param name="match_part_select" value="false"/>
706 <param name="match_part_select" value="false"/> 704 </conditional>
707 </conditional> 705 <section name="jbcolor_scale">
708 <section name="jbcolor_scale"> 706 <conditional name="color_score">
709 <conditional name="color_score"> 707 <param name="color_score_select" value="score"/>
710 <param name="color_score_select" value="score"/> 708 <param name="score_scaling" value="linear"/>
711 <param name="score_scaling" value="linear"/> 709 <conditional name="score_scales">
712 <conditional name="score_scales"> 710 <param name="scale_select" value="manual"/>
713 <param name="scale_select" value="manual"/> 711 <param name="minimum" value="0"/>
714 <param name="minimum" value="0"/> 712 <param name="maximum" value="1000"/>
715 <param name="maximum" value="1000"/> 713 </conditional>
716 </conditional> 714 <conditional name="color_scheme">
717 <conditional name="color_scheme"> 715 <param name="score_scheme" value="opacity"/>
718 <param name="score_scheme" value="opacity"/> 716 <conditional name="color">
719 <conditional name="color"> 717 <param name="color_select" value="automatic"/>
720 <param name="color_select" value="automatic"/> 718 </conditional>
721 </conditional> 719 </conditional>
722 </conditional> 720 </conditional>
723 </conditional> 721 </section>
724 </section> 722 </conditional>
725 </conditional> 723 </repeat>
726 </repeat> 724 <repeat name="data_tracks">
727 <repeat name="data_tracks"> 725 <conditional name="data_format">
728 <conditional name="data_format"> 726 <param name="data_format_select" value="gff"/>
729 <param name="data_format_select" value="gff"/> 727 <conditional name="useuri">
730 <conditional name="useuri"> 728 <param name="annotation" value="gff3/1.gff"/>
731 <param name="annotation" value="gff3/1.gff"/> 729 <param name="insource" value= "history"/>
732 <param name="insource" value= "history"/> 730 </conditional>
733 </conditional> 731 <conditional name="match_part">
734 <conditional name="match_part"> 732 <param name="match_part_select" value="false"/>
735 <param name="match_part_select" value="false"/> 733 </conditional>
736 </conditional> 734 <section name="jbcolor_scale">
737 <section name="jbcolor_scale"> 735 <conditional name="color_score">
738 <conditional name="color_score"> 736 <param name="color_score_select" value="score"/>
739 <param name="color_score_select" value="score"/> 737 <param name="score_scaling" value="linear"/>
740 <param name="score_scaling" value="linear"/> 738 <conditional name="score_scales">
741 <conditional name="score_scales"> 739 <param name="scale_select" value="manual"/>
742 <param name="scale_select" value="manual"/> 740 <param name="minimum" value="0"/>
743 <param name="minimum" value="0"/> 741 <param name="maximum" value="1000"/>
744 <param name="maximum" value="1000"/> 742 </conditional>
745 </conditional> 743 <conditional name="color_scheme">
746 <conditional name="color_scheme"> 744 <param name="score_scheme" value="opacity"/>
747 <param name="score_scheme" value="opacity"/> 745 <conditional name="color">
748 <conditional name="color"> 746 <param name="color_select" value="manual"/>
749 <param name="color_select" value="manual"/> 747 <param name="style_color" value="#ff0000"/>
750 <param name="style_color" value="#ff0000"/> 748 </conditional>
751 </conditional> 749 </conditional>
752 </conditional> 750 </conditional>
753 </conditional> 751 </section>
754 </section> 752 </conditional>
755 </conditional> 753 </repeat>
756 </repeat> 754 </repeat>
757 </repeat> 755 <repeat name="track_groups">
758
759 <repeat name="track_groups">
760 <param name="category" value="Realistic" /> 756 <param name="category" value="Realistic" />
761 <repeat name="data_tracks"> 757 <repeat name="data_tracks">
762 <conditional name="data_format"> 758 <conditional name="data_format">
763 <param name="data_format_select" value="gff"/> 759 <param name="data_format_select" value="gff"/>
764 <conditional name="useuri"> 760 <conditional name="useuri">
765 <param name="annotation" value="gff3/interpro.gff"/> 761 <param name="annotation" value="gff3/interpro.gff"/>
766 <param name="insource" value= "history"/> 762 <param name="insource" value= "history"/>
767 </conditional> 763 </conditional>
768 <conditional name="match_part"> 764 <conditional name="match_part">
769 <param name="match_part_select" value="false"/> 765 <param name="match_part_select" value="false"/>
770 </conditional> 766 </conditional>
771 <section name="jbcolor_scale"> 767 <section name="jbcolor_scale">
772 <conditional name="color_score"> 768 <conditional name="color_score">
773 <param name="color_score_select" value="none"/> 769 <param name="color_score_select" value="none"/>
774 </conditional> 770 </conditional>
775 <conditional name="color"> 771 <conditional name="color">
776 <param name="color_select" value="automatic"/> 772 <param name="color_select" value="automatic"/>
777 </conditional> 773 </conditional>
778 </section> 774 </section>
779 </conditional> 775 </conditional>
780 </repeat> 776 </repeat>
781 <repeat name="data_tracks"> 777 <repeat name="data_tracks">
782 <conditional name="data_format"> 778 <conditional name="data_format">
783 <param name="data_format_select" value="gff"/> 779 <param name="data_format_select" value="gff"/>
784 <conditional name="useuri"> 780 <conditional name="useuri">
785 <param name="annotation" value="gff3/2.gff"/> 781 <param name="annotation" value="gff3/2.gff"/>
786 <param name="insource" value= "history"/> 782 <param name="insource" value= "history"/>
796 <conditional name="color"> 792 <conditional name="color">
797 <param name="color_select" value="automatic"/> 793 <param name="color_select" value="automatic"/>
798 </conditional> 794 </conditional>
799 </section> 795 </section>
800 </conditional> 796 </conditional>
797 </repeat>
801 </repeat> 798 </repeat>
802 </repeat> 799 </repeat>
803 800
804 <param name="uglyTestingHack" value="enabled" /> 801 <param name="uglyTestingHack" value="enabled" />
805 <output name="output"> 802 <output name="output">
806 <assert_contents> 803 <assert_contents>
807 <has_text text="Auto Coloured"/> 804 <has_text text="Ignore Scale"/>
808 <has_text text="A.gff"/> 805 <has_text text="A.gff"/>
809 <has_text text="B.gff"/> 806 <has_text text="B.gff"/>
810 <has_text text="C.gff"/> 807 <has_text text="C.gff"/>
811 <has_text text="interpro.gff"/> 808 <has_text text="interpro.gff"/>
812 <has_text text="Scaled Colour"/> 809 <has_text text="Scaled Colour"/>
813 <has_text text="1.gff"/> 810 <has_text text="1.gff"/>
814 <has_text text="2.gff"/> 811 <has_text text="2.gff"/>
815 </assert_contents> 812 </assert_contents>
816 </output> 813 </output>
817 </test> 814 </test>
818 <test> 815
819 <repeat name="assemblies">
820 <conditional name="reference_genome">
821 <param name="genome_type_select" value="history"/>
822 <param name="genome" value="merlin.fa"/>
823 <param name="genome.ext" value="fasta"/>
824 <param name="genome.name" value="Merlin"/>
825 </conditional>
826 <repeat name="track_groups">
827 <param name="category" value="Default" />
828 <repeat name="data_tracks">
829 <conditional name="data_format">
830 <param name="data_format_select" value="gff"/>
831 <conditional name="useuri">
832 <param name="annotation" value="gff3/1.gff"/>
833 <param name="insource" value= "history"/>
834 </conditional>
835 <conditional name="match_part">
836 <param name="match_part_select" value="false"/>
837 </conditional>
838 <section name="jbcolor_scale">
839 <conditional name="color_score">
840 <param name="color_score_select" value="none"/>
841 </conditional>
842 <conditional name="color">
843 <param name="color_select" value="automatic"/>
844 </conditional>
845 </section>
846 <section name="jbmenu">
847 <repeat name="track_menu">
848 <param name="menu_action" value="iframeDialog"/>
849 <param name="menu_label" value="Some menu item"/>
850 <param name="menu_title" value="Frame title"/>
851 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
852 <param name="menu_icon" value="dijitIconNewTask"/>
853 </repeat>
854 <repeat name="track_menu">
855 <param name="menu_action" value="newWindow"/>
856 <param name="menu_label" value="Another menu item"/>
857 <param name="menu_title" value="Frame title 2"/>
858 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
859 </repeat>
860 </section>
861 </conditional>
862 </repeat>
863 <repeat name="data_tracks">
864 <conditional name="data_format">
865 <param name="data_format_select" value="gff"/>
866 <conditional name="useuri">
867 <param name="annotation" value="gff3/1.gff"/>
868 <param name="insource" value= "history"/>
869 </conditional>
870 <conditional name="match_part">
871 <param name="match_part_select" value="false"/>
872 </conditional>
873 <section name="jbcolor_scale">
874 <conditional name="color_score">
875 <param name="color_score_select" value="none"/>
876 </conditional>
877 <conditional name="color">
878 <param name="color_select" value="automatic"/>
879 </conditional>
880 </section>
881 </conditional>
882 </repeat>
883 </repeat>
884 </repeat>
885 <param name="uglyTestingHack" value="enabled" />
886 <output name="output">
887 <assert_contents>
888 <has_text text="With menu or index"/>
889 <has_text text="gff"/>
890 </assert_contents>
891 </output>
892 </test>
893 816
894 <!-- TODO add a synteny test --> 817 <!-- TODO add a synteny test -->
895 <!-- TODO add a bam and a cram test --> 818 <!-- TODO add a bam and a cram test -->
896 <!-- TODO add an hic test --> 819 <!-- TODO add an hic test -->
897 <!-- TODO add a vcf_bgzip test --> 820 <!-- TODO add a vcf_bgzip test -->