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comparison plot.xml @ 7:e0e6334749cf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 12:18:03 +0000
parents 7c8b155300d4
children d2a2adbb0ef3
comparison
equal deleted inserted replaced
6:7c8b155300d4 7:e0e6334749cf
23 sc.pl.scatter( 23 sc.pl.scatter(
24 @CMD_param_plot_inputs@ 24 @CMD_param_plot_inputs@
25 #if $method.type.type == 'xy' 25 #if $method.type.type == 'xy'
26 x='$method.type.x', 26 x='$method.type.x',
27 y='$method.type.y', 27 y='$method.type.y',
28 #if str($method.type.color) != ''
29 color='$method.type.color',
30 #end if
28 #if str('$method.type.layers.use_layers') == 'true' 31 #if str('$method.type.layers.use_layers') == 'true'
29 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'), 32 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
30 #end if 33 #end if
31 #else 34 #else
32 basis='$method.type.basis', 35 basis='$method.type.basis',
39 sort_order=$method.sort_order, 42 sort_order=$method.sort_order,
40 @CMD_params_groups@ 43 @CMD_params_groups@
41 @CMD_params_pl_components@ 44 @CMD_params_pl_components@
42 projection='$method.plot.projection', 45 projection='$method.plot.projection',
43 legend_loc='$method.plot.legend_loc', 46 legend_loc='$method.plot.legend_loc',
47 #if $method.plot.palette != 'default'
48 palette='$method.plot.palette',
49 #end if
50 #if $method.plot.color_map != 'None'
51 color_map='$method.plot.color_map',
52 #end if
44 @CMD_param_legend_fontsize@ 53 @CMD_param_legend_fontsize@
45 legend_fontweight='$method.plot.legend_fontweight', 54 legend_fontweight='$method.plot.legend_fontweight',
46 color_map='$method.plot.color_map',
47 #if str($method.plot.palette) != ''
48 palette='$method.plot.palette',
49 #end if
50 frameon=$method.plot.frameon,
51 @CMD_param_title@ 55 @CMD_param_title@
52 @CMD_param_size@) 56 @CMD_param_size@
57 frameon=$method.plot.frameon)
53 58
54 #else if $method.method == 'pl.heatmap' 59 #else if $method.method == 'pl.heatmap'
55 sc.pl.heatmap( 60 sc.pl.heatmap(
56 @CMD_param_plot_inputs@ 61 @CMD_param_plot_inputs@
57 @CMD_params_inputs@ 62 @CMD_params_inputs@
410 <param name="type" type="select" label="Plotting tool that computed coordinates" help=""> 415 <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
411 <option value="xy">Using coordinates</option> 416 <option value="xy">Using coordinates</option>
412 <option value="basis">Using tool that computes coordinates</option> 417 <option value="basis">Using tool that computes coordinates</option>
413 </param> 418 </param>
414 <when value="xy"> 419 <when value="xy">
415 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'"/> 420 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
416 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'"/> 421 <expand macro="sanitize_query" />
422 </param>
423 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
424 <expand macro="sanitize_query" />
425 </param>
426 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
427 <expand macro="sanitize_query" />
428 </param>
417 <conditional name="layers"> 429 <conditional name="layers">
418 <param argument="use_layers" type="select" label="Use the layers attribute?"> 430 <param argument="use_layers" type="select" label="Use the layers attribute?">
419 <option value="true">Yes</option> 431 <option value="true">Yes</option>
420 <option value="false" selected="true">No</option> 432 <option value="false" selected="true">No</option>
421 </param> 433 </param>
422 <when value="true"> 434 <when value="true">
423 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present"/> 435 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
424 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present"/> 436 <expand macro="sanitize_query" />
425 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present"/> 437 </param>
438 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
439 <expand macro="sanitize_query" />
440 </param>
441 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
442 <expand macro="sanitize_query" />
443 </param>
426 </when> 444 </when>
427 <when value="false"/> 445 <when value="false"/>
428 </conditional> 446 </conditional>
429 </when> 447 </when>
430 <when value="basis"> 448 <when value="basis">
472 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option> 490 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
473 </param> 491 </param>
474 <when value="var_names"/> 492 <when value="var_names"/>
475 <when value="obs"/> 493 <when value="obs"/>
476 <when value="custom"> 494 <when value="custom">
477 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/> 495 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
496 <expand macro="sanitize_query" />
497 </param>
478 </when> 498 </when>
479 </conditional> 499 </conditional>
480 <expand macro="param_groupby"/> 500 <expand macro="param_groupby"/>
481 <expand macro="param_log"/> 501 <expand macro="param_log"/>
482 <expand macro="param_use_raw"/> 502 <expand macro="param_use_raw"/>
493 </when> 513 </when>
494 <when value="False"/> 514 <when value="False"/>
495 </conditional> 515 </conditional>
496 <expand macro="param_scale"/> 516 <expand macro="param_scale"/>
497 </section> 517 </section>
498 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown."/> 518 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown.">
519 <expand macro="sanitize_query" />
520 </param>
499 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/> 521 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
500 <expand macro="seaborn_violinplot"/> 522 <expand macro="seaborn_violinplot"/>
501 </when> 523 </when>
502 <when value="pl.stacked_violin"> 524 <when value="pl.stacked_violin">
503 <expand macro="params_inputs"/> 525 <expand macro="params_inputs"/>
508 <expand macro="params_inputs"/> 530 <expand macro="params_inputs"/>
509 <expand macro="params_plots"/> 531 <expand macro="params_plots"/>
510 <expand macro="pl_matrixplot"/> 532 <expand macro="pl_matrixplot"/>
511 </when> 533 </when>
512 <when value="pl.clustermap"> 534 <when value="pl.clustermap">
513 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/> 535 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">
536 <expand macro="sanitize_query" />
537 </param>
514 <expand macro="param_use_raw"/> 538 <expand macro="param_use_raw"/>
515 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap"> 539 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
516 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html"> 540 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
517 <option value="single">single: Nearest Point Algorithm</option> 541 <option value="single">single: Nearest Point Algorithm</option>
518 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option> 542 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
543 <expand macro="param_log"/> 567 <expand macro="param_log"/>
544 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/> 568 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
545 </when> 569 </when>
546 <when value="pl.highest_expr_genes"> 570 <when value="pl.highest_expr_genes">
547 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/> 571 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
548 <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'."/> 572 <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'.">
573 <expand macro="sanitize_query" />
574 </param>
549 <section name="setseaborn_boxplot" title="Plot settings" expanded="false"> 575 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
550 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/> 576 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help="">
577 <expand macro="sanitize_query" />
578 </param>
551 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details."> 579 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
552 <expand macro="seaborn_color_palette_options"/> 580 <expand macro="seaborn_color_palette_options"/>
553 </param> 581 </param>
554 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/> 582 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
555 </section> 583 </section>
561 <expand macro="param_groups"/> 589 <expand macro="param_groups"/>
562 <expand macro="pl_attribute_section"/> 590 <expand macro="pl_attribute_section"/>
563 <expand macro="section_matplotlib_pyplot_scatter"/> 591 <expand macro="section_matplotlib_pyplot_scatter"/>
564 </when> 592 </when>
565 <when value="pl.pca_loadings"> 593 <when value="pl.pca_loadings">
566 <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components"/> 594 <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">
595 <expand macro="sanitize_query" />
596 </param>
567 </when> 597 </when>
568 <when value="pl.pca_variance_ratio"> 598 <when value="pl.pca_variance_ratio">
569 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/> 599 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
570 <expand macro="param_log"/> 600 <expand macro="param_log"/>
571 </when> 601 </when>
640 <when value="pl.paga_compare"> 670 <when value="pl.paga_compare">
641 <expand macro="inputs_paga"/> 671 <expand macro="inputs_paga"/>
642 </when> 672 </when>
643 <when value="pl.paga_path"> 673 <when value="pl.paga_path">
644 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" 674 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
645 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/> 675 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">
646 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/> 676 <expand macro="sanitize_query" />
677 </param>
678 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
679 <expand macro="sanitize_query" />
680 </param>
647 <expand macro="param_use_raw"/> 681 <expand macro="param_use_raw"/>
648 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/> 682 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated">
683 <expand macro="sanitize_query" />
684 </param>
649 <expand macro="param_color_map"/> 685 <expand macro="param_color_map"/>
650 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/> 686 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
651 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups"/> 687 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">
688 <expand macro="sanitize_query" />
689 </param>
652 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/> 690 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
653 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/> 691 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
654 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/> 692 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
655 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/> 693 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
656 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/> 694 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>
672 </param> 710 </param>
673 <when value="n_genes"> 711 <when value="n_genes">
674 <expand macro="param_n_genes"/> 712 <expand macro="param_n_genes"/>
675 </when> 713 </when>
676 <when value="gene_names"> 714 <when value="gene_names">
677 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names"/> 715 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
716 <expand macro="sanitize_query" />
717 </param>
678 </when> 718 </when>
679 </conditional> 719 </conditional>
680 <expand macro="gene_symbols"/> 720 <expand macro="gene_symbols"/>
681 <expand macro="param_use_raw"/> 721 <expand macro="param_use_raw"/>
682 <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/> 722 <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>