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comparison inspect.xml @ 6:5e9171dc8244 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:25:37 -0500
parents 08192eebb47d
children 6c145a6868cc
comparison
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5:08192eebb47d 6:5e9171dc8244
459 <param argument="max_value" type="float" value="" optional="true" label="Maximum value" 459 <param argument="max_value" type="float" value="" optional="true" label="Maximum value"
460 help="Clip (truncate) to this value after scaling. If not set, it does not clip."/> 460 help="Clip (truncate) to this value after scaling. If not set, it does not clip."/>
461 </when> 461 </when>
462 <when value="pp.sqrt"/> 462 <when value="pp.sqrt"/>
463 </conditional> 463 </conditional>
464 <expand macro="inputs_common_advanced"/>
464 </inputs> 465 </inputs>
465 <outputs> 466 <outputs>
466 <expand macro="anndata_outputs"/> 467 <expand macro="anndata_outputs"/>
467 </outputs> 468 </outputs>
468 <tests> 469 <tests>
469 <test> 470 <test>
470 <!-- test 1 --> 471 <!-- test 0 -->
471 <param name="adata" value="sparce_csr_matrix.h5ad" /> 472 <param name="adata" value="sparce_csr_matrix.h5ad" />
472 <conditional name="method"> 473 <conditional name="method">
473 <param name="method" value="pp.calculate_qc_metrics"/> 474 <param name="method" value="pp.calculate_qc_metrics"/>
474 <param name="expr_type" value="counts"/> 475 <param name="expr_type" value="counts"/>
475 <param name="var_type" value="genes"/> 476 <param name="var_type" value="genes"/>
476 <param name="qc_vars" value="mito,negative"/> 477 <param name="qc_vars" value="mito,negative"/>
477 <param name="percent_top" value=""/> 478 <param name="percent_top" value=""/>
478 </conditional> 479 </conditional>
479 <assert_stdout> 480 <section name="advanced_common">
480 <has_text_matching expression="sc.pp.calculate_qc_metrics" /> 481 <param name="show_log" value="true" />
481 <has_text_matching expression="expr_type='counts'" /> 482 </section>
482 <has_text_matching expression="var_type='genes'" /> 483 <output name="hidden_output">
483 <has_text_matching expression="qc_vars=\['mito', 'negative'\]" /> 484 <assert_contents>
484 </assert_stdout> 485 <has_text_matching expression="sc.pp.calculate_qc_metrics" />
486 <has_text_matching expression="expr_type='counts'" />
487 <has_text_matching expression="var_type='genes'" />
488 <has_text_matching expression="qc_vars=\['mito', 'negative'\]" />
489 </assert_contents>
490 </output>
485 <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/> 491 <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>
486 </test> 492 </test>
487 <test> 493 <test>
488 <!-- test 2 --> 494 <!-- test 1 -->
489 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> 495 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
490 <conditional name="method"> 496 <conditional name="method">
491 <param name="method" value="pp.neighbors"/> 497 <param name="method" value="pp.neighbors"/>
492 <param name="n_neighbors" value="15"/> 498 <param name="n_neighbors" value="15"/>
493 <param name="knn" value="True"/> 499 <param name="knn" value="True"/>
494 <param name="random_state" value="0"/> 500 <param name="random_state" value="0"/>
495 <param name="pp_neighbors_method" value="umap"/> 501 <param name="pp_neighbors_method" value="umap"/>
496 <param name="metric" value="euclidean"/> 502 <param name="metric" value="euclidean"/>
497 </conditional> 503 </conditional>
498 <assert_stdout> 504 <section name="advanced_common">
499 <has_text_matching expression="sc.pp.neighbors"/> 505 <param name="show_log" value="true" />
500 <has_text_matching expression="n_neighbors=15"/> 506 </section>
501 <has_text_matching expression="knn=True"/> 507 <output name="hidden_output">
502 <has_text_matching expression="random_state=0"/> 508 <assert_contents>
503 <has_text_matching expression="method='umap'"/> 509 <has_text_matching expression="sc.pp.neighbors"/>
504 <has_text_matching expression="metric='euclidean'"/> 510 <has_text_matching expression="n_neighbors=15"/>
505 </assert_stdout> 511 <has_text_matching expression="knn=True"/>
512 <has_text_matching expression="random_state=0"/>
513 <has_text_matching expression="method='umap'"/>
514 <has_text_matching expression="metric='euclidean'"/>
515 </assert_contents>
516 </output>
506 <output name="anndata_out" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"> 517 <output name="anndata_out" file="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
507 <assert_contents> 518 <assert_contents>
508 <has_h5_keys keys="X, obs, obsm, uns, var" /> 519 <has_h5_keys keys="X, obs, obsm, uns, var" />
509 </assert_contents> 520 </assert_contents>
510 </output> 521 </output>
511 </test> 522 </test>
512 <test> 523 <test>
513 <!-- test 3 --> 524 <!-- test 2 -->
514 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" /> 525 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />
515 <conditional name="method"> 526 <conditional name="method">
516 <param name="method" value="pp.neighbors"/> 527 <param name="method" value="pp.neighbors"/>
517 <param name="n_neighbors" value="15"/> 528 <param name="n_neighbors" value="15"/>
518 <param name="knn" value="True"/> 529 <param name="knn" value="True"/>
519 <param name="pp_neighbors_method" value="gauss"/> 530 <param name="pp_neighbors_method" value="gauss"/>
520 <param name="metric" value="braycurtis"/> 531 <param name="metric" value="braycurtis"/>
521 </conditional> 532 </conditional>
522 <assert_stdout> 533 <section name="advanced_common">
523 <has_text_matching expression="sc.pp.neighbors"/> 534 <param name="show_log" value="true" />
524 <has_text_matching expression="n_neighbors=15"/> 535 </section>
525 <has_text_matching expression="knn=True"/> 536 <output name="hidden_output">
526 <has_text_matching expression="random_state=0"/> 537 <assert_contents>
527 <has_text_matching expression="method='gauss'"/> 538 <has_text_matching expression="sc.pp.neighbors"/>
528 <has_text_matching expression="metric='braycurtis'"/> 539 <has_text_matching expression="n_neighbors=15"/>
529 </assert_stdout> 540 <has_text_matching expression="knn=True"/>
541 <has_text_matching expression="random_state=0"/>
542 <has_text_matching expression="method='gauss'"/>
543 <has_text_matching expression="metric='braycurtis'"/>
544 </assert_contents>
545 </output>
530 <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 546 <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
531 </test> 547 </test>
532 <test> 548 <test>
533 <!-- test 4 --> 549 <!-- test 3 -->
534 <param name="adata" value="krumsiek11.h5ad" /> 550 <param name="adata" value="krumsiek11.h5ad" />
535 <conditional name="method"> 551 <conditional name="method">
536 <param name="method" value="tl.score_genes"/> 552 <param name="method" value="tl.score_genes"/>
537 <param name="gene_list" value="Gata2, Fog1"/> 553 <param name="gene_list" value="Gata2, Fog1"/>
538 <param name="ctrl_size" value="2"/> 554 <param name="ctrl_size" value="2"/>
539 <param name="n_bins" value="2"/> 555 <param name="n_bins" value="2"/>
540 <param name="random_state" value="2"/> 556 <param name="random_state" value="2"/>
541 <param name="use_raw" value="False"/> 557 <param name="use_raw" value="False"/>
542 <param name="score_name" value="score"/> 558 <param name="score_name" value="score"/>
543 </conditional> 559 </conditional>
544 <assert_stdout> 560 <section name="advanced_common">
545 <has_text_matching expression="sc.tl.score_genes" /> 561 <param name="show_log" value="true" />
546 <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" /> 562 </section>
547 <has_text_matching expression="ctrl_size=2" /> 563 <output name="hidden_output">
548 <has_text_matching expression="score_name='score'" /> 564 <assert_contents>
549 <has_text_matching expression="n_bins=2" /> 565 <has_text_matching expression="sc.tl.score_genes" />
550 <has_text_matching expression="random_state=2" /> 566 <has_text_matching expression="gene_list=\['Gata2', 'Fog1'\]" />
551 <has_text_matching expression="use_raw=False" /> 567 <has_text_matching expression="ctrl_size=2" />
552 <has_text_matching expression="copy=False" /> 568 <has_text_matching expression="score_name='score'" />
553 </assert_stdout> 569 <has_text_matching expression="n_bins=2" />
570 <has_text_matching expression="random_state=2" />
571 <has_text_matching expression="use_raw=False" />
572 <has_text_matching expression="copy=False" />
573 </assert_contents>
574 </output>
554 <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 575 <output name="anndata_out" file="tl.score_genes.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
555 </test> 576 </test>
556 <test> 577 <test>
557 <!-- test 5 --> 578 <!-- test 4 -->
558 <param name="adata" value="krumsiek11.h5ad" /> 579 <param name="adata" value="krumsiek11.h5ad" />
559 <conditional name="method"> 580 <conditional name="method">
560 <param name="method" value="tl.score_genes_cell_cycle"/> 581 <param name="method" value="tl.score_genes_cell_cycle"/>
561 <conditional name='s_genes'> 582 <conditional name='s_genes'>
562 <param name="format" value="text"/> 583 <param name="format" value="text"/>
568 </conditional> 589 </conditional>
569 <param name="n_bins" value="2"/> 590 <param name="n_bins" value="2"/>
570 <param name="random_state" value="1"/> 591 <param name="random_state" value="1"/>
571 <param name="use_raw" value="False"/> 592 <param name="use_raw" value="False"/>
572 </conditional> 593 </conditional>
573 <assert_stdout> 594 <section name="advanced_common">
574 <has_text_matching expression="sc.tl.score_genes_cell_cycle"/> 595 <param name="show_log" value="true" />
575 <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> 596 </section>
576 <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/> 597 <output name="hidden_output">
577 <has_text_matching expression="n_bins=2"/> 598 <assert_contents>
578 <has_text_matching expression="random_state=1"/> 599 <has_text_matching expression="sc.tl.score_genes_cell_cycle"/>
579 <has_text_matching expression="use_raw=False"/> 600 <has_text_matching expression="s_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
580 </assert_stdout> 601 <has_text_matching expression="g2m_genes=\['Gata2', 'Fog1', 'EgrNab'\]"/>
602 <has_text_matching expression="n_bins=2"/>
603 <has_text_matching expression="random_state=1"/>
604 <has_text_matching expression="use_raw=False"/>
605 </assert_contents>
606 </output>
581 <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 607 <output name="anndata_out" file="tl.score_genes_cell_cycle.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
582 </test> 608 </test>
583 <test> 609 <test>
584 <!-- test 6 --> 610 <!-- test 5 -->
585 <param name="adata" value="krumsiek11.h5ad" /> 611 <param name="adata" value="krumsiek11.h5ad" />
586 <conditional name="method"> 612 <conditional name="method">
587 <param name="method" value="tl.rank_genes_groups"/> 613 <param name="method" value="tl.rank_genes_groups"/>
588 <param name="groupby" value="cell_type"/> 614 <param name="groupby" value="cell_type"/>
589 <param name="use_raw" value="True"/> 615 <param name="use_raw" value="True"/>
594 <conditional name="tl_rank_genes_groups_method"> 620 <conditional name="tl_rank_genes_groups_method">
595 <param name="method" value="t-test_overestim_var"/> 621 <param name="method" value="t-test_overestim_var"/>
596 <param name="corr_method" value="benjamini-hochberg"/> 622 <param name="corr_method" value="benjamini-hochberg"/>
597 </conditional> 623 </conditional>
598 </conditional> 624 </conditional>
599 <assert_stdout> 625 <section name="advanced_common">
600 <has_text_matching expression="sc.tl.rank_genes_groups"/> 626 <param name="show_log" value="true" />
601 <has_text_matching expression="groupby='cell_type'"/> 627 </section>
602 <has_text_matching expression="use_raw=True"/> 628 <output name="hidden_output">
603 <has_text_matching expression="reference='rest'"/> 629 <assert_contents>
604 <has_text_matching expression="n_genes=100"/> 630 <has_text_matching expression="sc.tl.rank_genes_groups"/>
605 <has_text_matching expression="method='t-test_overestim_var'"/> 631 <has_text_matching expression="groupby='cell_type'"/>
606 <has_text_matching expression="corr_method='benjamini-hochberg'"/> 632 <has_text_matching expression="use_raw=True"/>
607 </assert_stdout> 633 <has_text_matching expression="reference='rest'"/>
634 <has_text_matching expression="n_genes=100"/>
635 <has_text_matching expression="method='t-test_overestim_var'"/>
636 <has_text_matching expression="corr_method='benjamini-hochberg'"/>
637 </assert_contents>
638 </output>
608 <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 639 <output name="anndata_out" file="tl.rank_genes_groups.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
609 </test> 640 </test>
610 <test> 641 <test>
611 <!-- test 7 --> 642 <!-- test 6 -->
612 <param name="adata" value="pbmc68k_reduced.h5ad" /> 643 <param name="adata" value="pbmc68k_reduced.h5ad" />
613 <conditional name="method"> 644 <conditional name="method">
614 <param name="method" value="tl.rank_genes_groups"/> 645 <param name="method" value="tl.rank_genes_groups"/>
615 <param name="groupby" value="louvain"/> 646 <param name="groupby" value="louvain"/>
616 <param name="use_raw" value="True"/> 647 <param name="use_raw" value="True"/>
628 </conditional> 659 </conditional>
629 <param name="tol" value="1e-4"/> 660 <param name="tol" value="1e-4"/>
630 <param name="c" value="1.0"/> 661 <param name="c" value="1.0"/>
631 </conditional> 662 </conditional>
632 </conditional> 663 </conditional>
633 <assert_stdout> 664 <section name="advanced_common">
634 <has_text_matching expression="sc.tl.rank_genes_groups"/> 665 <param name="show_log" value="true" />
635 <has_text_matching expression="groupby='louvain'"/> 666 </section>
636 <has_text_matching expression="use_raw=True"/> 667 <output name="hidden_output">
637 <has_text_matching expression="reference='rest'"/> 668 <assert_contents>
638 <has_text_matching expression="n_genes=100"/> 669 <has_text_matching expression="sc.tl.rank_genes_groups"/>
639 <has_text_matching expression="method='logreg'"/> 670 <has_text_matching expression="groupby='louvain'"/>
640 <has_text_matching expression="solver='newton-cg'"/> 671 <has_text_matching expression="use_raw=True"/>
641 <has_text_matching expression="penalty='l2'"/> 672 <has_text_matching expression="reference='rest'"/>
642 <has_text_matching expression="fit_intercept=True"/> 673 <has_text_matching expression="n_genes=100"/>
643 <has_text_matching expression="max_iter=100"/> 674 <has_text_matching expression="method='logreg'"/>
644 <has_text_matching expression="multi_class='auto'"/> 675 <has_text_matching expression="solver='newton-cg'"/>
645 <has_text_matching expression="tol=0.0001"/> 676 <has_text_matching expression="penalty='l2'"/>
646 <has_text_matching expression="C=1.0"/> 677 <has_text_matching expression="fit_intercept=True"/>
647 </assert_stdout> 678 <has_text_matching expression="max_iter=100"/>
679 <has_text_matching expression="multi_class='auto'"/>
680 <has_text_matching expression="tol=0.0001"/>
681 <has_text_matching expression="C=1.0"/>
682 </assert_contents>
683 </output>
648 <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size"> 684 <output name="anndata_out" file="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad" ftype="h5ad" compare="sim_size">
649 <assert_contents> 685 <assert_contents>
650 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> 686 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
651 </assert_contents> 687 </assert_contents>
652 </output> 688 </output>
653 </test> 689 </test>
654 <test> 690 <test>
655 <!-- test 8 --> 691 <!-- test 7 -->
656 <param name="adata" value="pbmc68k_reduced.h5ad" /> 692 <param name="adata" value="pbmc68k_reduced.h5ad" />
657 <conditional name="method"> 693 <conditional name="method">
658 <param name="method" value="tl.rank_genes_groups"/> 694 <param name="method" value="tl.rank_genes_groups"/>
659 <param name="groupby" value="louvain"/> 695 <param name="groupby" value="louvain"/>
660 <param name="use_raw" value="True"/> 696 <param name="use_raw" value="True"/>
678 </conditional> 714 </conditional>
679 <param name="tol" value="1e-4"/> 715 <param name="tol" value="1e-4"/>
680 <param name="c" value="1.0"/> 716 <param name="c" value="1.0"/>
681 </conditional> 717 </conditional>
682 </conditional> 718 </conditional>
683 <assert_stdout> 719 <section name="advanced_common">
684 <has_text_matching expression="sc.tl.rank_genes_groups"/> 720 <param name="show_log" value="true" />
685 <has_text_matching expression="groupby='louvain'"/> 721 </section>
686 <has_text_matching expression="use_raw=True"/> 722 <output name="hidden_output">
687 <has_text_matching expression="reference='rest'"/> 723 <assert_contents>
688 <has_text_matching expression="n_genes=100"/> 724 <has_text_matching expression="sc.tl.rank_genes_groups"/>
689 <has_text_matching expression="method='logreg'"/> 725 <has_text_matching expression="groupby='louvain'"/>
690 <has_text_matching expression="solver='liblinear'"/> 726 <has_text_matching expression="use_raw=True"/>
691 <has_text_matching expression="penalty='l2'"/> 727 <has_text_matching expression="reference='rest'"/>
692 <has_text_matching expression="dual=False"/> 728 <has_text_matching expression="n_genes=100"/>
693 <has_text_matching expression="fit_intercept=True"/> 729 <has_text_matching expression="method='logreg'"/>
694 <has_text_matching expression="intercept_scaling=1.0"/> 730 <has_text_matching expression="solver='liblinear'"/>
695 <has_text_matching expression="tol=0.0001"/> 731 <has_text_matching expression="penalty='l2'"/>
696 <has_text_matching expression="C=1.0"/> 732 <has_text_matching expression="dual=False"/>
697 </assert_stdout> 733 <has_text_matching expression="fit_intercept=True"/>
734 <has_text_matching expression="intercept_scaling=1.0"/>
735 <has_text_matching expression="tol=0.0001"/>
736 <has_text_matching expression="C=1.0"/>
737 </assert_contents>
738 </output>
698 <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"> 739 <output name="anndata_out" file="tl.rank_genes_groups.liblinear.krumsiek11.h5ad" ftype="h5ad" compare="sim_size">
699 <assert_contents> 740 <assert_contents>
700 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" /> 741 <has_h5_keys keys="X, obs, obsm, raw.X, raw.var, uns, var" />
701 </assert_contents> 742 </assert_contents>
702 </output> 743 </output>
729 <has_text_matching expression="method='overlap_count'"/> 770 <has_text_matching expression="method='overlap_count'"/>
730 </assert_stdout> 771 </assert_stdout>
731 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 772 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
732 </test>--> 773 </test>-->
733 <test> 774 <test>
775 <!-- test 8 -->
776 <param name="adata" value="krumsiek11.h5ad" />
777 <conditional name="method">
778 <param name="method" value="pp.log1p"/>
779 </conditional>
780 <section name="advanced_common">
781 <param name="show_log" value="true" />
782 </section>
783 <output name="hidden_output">
784 <assert_contents>
785 <has_text_matching expression="sc.pp.log1p"/>
786 </assert_contents>
787 </output>
788 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
789 </test>
790 <test>
734 <!-- test 9 --> 791 <!-- test 9 -->
735 <param name="adata" value="krumsiek11.h5ad" /> 792 <param name="adata" value="krumsiek11.h5ad" />
736 <conditional name="method"> 793 <conditional name="method">
737 <param name="method" value="pp.log1p"/>
738 </conditional>
739 <assert_stdout>
740 <has_text_matching expression="sc.pp.log1p"/>
741 </assert_stdout>
742 <output name="anndata_out" file="pp.log1p.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
743 </test>
744 <test>
745 <!-- test 10 -->
746 <param name="adata" value="krumsiek11.h5ad" />
747 <conditional name="method">
748 <param name="method" value="pp.scale"/> 794 <param name="method" value="pp.scale"/>
749 <param name="zero_center" value="true"/> 795 <param name="zero_center" value="true"/>
750 </conditional> 796 </conditional>
751 <assert_stdout> 797 <section name="advanced_common">
752 <has_text_matching expression="sc.pp.scale"/> 798 <param name="show_log" value="true" />
753 <has_text_matching expression="zero_center=True"/> 799 </section>
754 </assert_stdout> 800 <output name="hidden_output">
801 <assert_contents>
802 <has_text_matching expression="sc.pp.scale"/>
803 <has_text_matching expression="zero_center=True"/>
804 </assert_contents>
805 </output>
755 <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 806 <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
756 </test> 807 </test>
757 <test> 808 <test>
758 <!-- test 11 --> 809 <!-- test 10 -->
759 <param name="adata" value="krumsiek11.h5ad" /> 810 <param name="adata" value="krumsiek11.h5ad" />
760 <conditional name="method"> 811 <conditional name="method">
761 <param name="method" value="pp.scale"/> 812 <param name="method" value="pp.scale"/>
762 <param name="zero_center" value="true"/> 813 <param name="zero_center" value="true"/>
763 <param name="max_value" value="10"/> 814 <param name="max_value" value="10"/>
764 </conditional> 815 </conditional>
765 <assert_stdout> 816 <section name="advanced_common">
766 <has_text_matching expression="sc.pp.scale"/> 817 <param name="show_log" value="true" />
767 <has_text_matching expression="zero_center=True"/> 818 </section>
768 <has_text_matching expression="max_value=10.0"/> 819 <output name="hidden_output">
769 </assert_stdout> 820 <assert_contents>
821 <has_text_matching expression="sc.pp.scale"/>
822 <has_text_matching expression="zero_center=True"/>
823 <has_text_matching expression="max_value=10.0"/>
824 </assert_contents>
825 </output>
770 <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 826 <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
771 </test> 827 </test>
772 <test> 828 <test>
773 <!-- test 12 --> 829 <!-- test 11 -->
774 <param name="adata" value="krumsiek11.h5ad" /> 830 <param name="adata" value="krumsiek11.h5ad" />
775 <conditional name="method"> 831 <conditional name="method">
776 <param name="method" value="pp.sqrt"/> 832 <param name="method" value="pp.sqrt"/>
777 </conditional> 833 </conditional>
778 <assert_stdout> 834 <section name="advanced_common">
779 <has_text_matching expression="sc.pp.sqrt"/> 835 <param name="show_log" value="true" />
780 </assert_stdout> 836 </section>
837 <output name="hidden_output">
838 <assert_contents>
839 <has_text_matching expression="sc.pp.sqrt"/>
840 </assert_contents>
841 </output>
781 <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 842 <output name="anndata_out" file="pp.sqrt.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
782 </test> 843 </test>
783 </tests> 844 </tests>
784 <help><![CDATA[ 845 <help><![CDATA[
785 Calculate quality control metrics., using `pp.calculate_qc_metrics` 846 Calculate quality control metrics., using `pp.calculate_qc_metrics`