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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:40:08 +0000
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1 <tool id="seurat_plot" name="Plot" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>with Seurat</description>
3 <macros>
4 <import>seurat_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[
9 @INPUT_OBJ_PREAMBLE@
10 seurat-plot.R
11 @INPUT_OBJECT@
12 @OUTPUT_PLOT@
13 --plot-type '$plot_type.plot_type_selector'
14
15
16 #if str($plot_type.plot_type_selector) == 'DimPlot':
17
18 #if $plot_type.dims
19 --dims '$plot_type.dims'
20 #end if
21
22
23 #if $plot_type.cells
24 --cells '$plot_type.cells'
25 #end if
26
27
28 #if $plot_type.cols
29 --cols '$plot_type.cols'
30 #end if
31
32
33 #if $plot_type.pt_size
34 --pt-size '$plot_type.pt_size'
35 #end if
36
37
38 #if $plot_type.reduction
39 --reduction '$plot_type.reduction'
40 #end if
41
42
43 #if $plot_type.group_by
44 --group-by '$plot_type.group_by'
45 #end if
46
47
48 #if $plot_type.split_by
49 --split-by '$plot_type.split_by'
50 #end if
51
52
53 #if $plot_type.shape_by
54 --shape-by '$plot_type.shape_by'
55 #end if
56
57
58 #if $plot_type.order
59 --order '$plot_type.order'
60 #end if
61
62 $plot_type.shuffle
63
64
65 --seed '$plot_type.seed'
66
67 $plot_type.label
68
69
70 --label-size '$plot_type.label_size'
71
72
73 --label-color '$plot_type.label_color'
74
75 $plot_type.label_box
76
77 $plot_type.repel
78
79
80 #if $plot_type.cells_highlight
81 --cells-highlight '$plot_type.cells_highlight'
82 #end if
83
84
85 #if $plot_type.cols_highlight
86 --cols-highlight '$plot_type.cols_highlight'
87 #end if
88
89
90 #if $plot_type.sizes_highlight
91 --sizes-highlight '$plot_type.sizes_highlight'
92 #end if
93
94
95 #if $plot_type.na_value
96 --na-value '$plot_type.na_value'
97 #end if
98
99
100 #if $plot_type.ncol
101 --ncol '$plot_type.ncol'
102 #end if
103
104 #elif str($plot_type.plot_type_selector) == 'DoHeatmap':
105
106 #if $plot_type.features
107 --features '$plot_type.features'
108 #end if
109
110
111 #if $plot_type.cells
112 --cells '$plot_type.cells'
113 #end if
114
115
116 #if $plot_type.group_by
117 --group-by '$plot_type.group_by'
118 #end if
119
120 $plot_type.group_bar
121
122
123 #if $plot_type.group_colors
124 --group-colors '$plot_type.group_colors'
125 #end if
126
127
128 #if $plot_type.disp_min
129 --disp-min '$plot_type.disp_min'
130 #end if
131
132
133 #if $plot_type.disp_max
134 --disp-max '$plot_type.disp_max'
135 #end if
136
137
138 --slot '$plot_type.slot'
139
140
141 #if $plot_type.assay
142 --assay '$plot_type.assay'
143 #end if
144
145 $plot_type.label
146
147
148 #if $plot_type.size
149 --size '$plot_type.size'
150 #end if
151
152
153 #if $plot_type.hjust
154 --hjust '$plot_type.hjust'
155 #end if
156
157
158 #if $plot_type.angle
159 --angle '$plot_type.angle'
160 #end if
161
162 $plot_type.raster
163
164 $plot_type.draw_lines
165
166
167 #if $plot_type.lines_width
168 --lines-width '$plot_type.lines_width'
169 #end if
170
171
172 #if $plot_type.group_bar_height
173 --group-bar-height '$plot_type.group_bar_height'
174 #end if
175
176 $plot_type.combine
177
178 #elif str($plot_type.plot_type_selector) == 'RidgePlot':
179
180 --features '$plot_type.features'
181
182
183 #if $plot_type.cols_ridgeplot
184 --cols-ridgeplot '$plot_type.cols_ridgeplot'
185 #end if
186
187
188 #if $plot_type.idents
189 --idents '$plot_type.idents'
190 #end if
191
192 $plot_type.sort
193
194
195 #if $plot_type.assay
196 --assay '$plot_type.assay'
197 #end if
198
199
200 #if $plot_type.group_by
201 --group-by '$plot_type.group_by'
202 #end if
203
204 $plot_type.same_y_lims
205
206 $plot_type.log
207
208
209 #if $plot_type.ncol
210 --ncol '$plot_type.ncol'
211 #end if
212
213
214 #if $plot_type.slot
215 --slot '$plot_type.slot'
216 #end if
217
218 $plot_type.stack
219
220
221 #if $plot_type.fill_by
222 --fill-by '$plot_type.fill_by'
223 #end if
224
225 #elif str($plot_type.plot_type_selector) == 'FeaturePlot':
226
227 --features '$plot_type.features'
228
229
230 #if $plot_type.dims
231 --dims '$plot_type.dims'
232 #end if
233
234
235 #if $plot_type.cells
236 --cells '$plot_type.cells'
237 #end if
238
239
240 #if $plot_type.cols_feature_plot
241 --cols-feature-plot '$plot_type.cols_feature_plot'
242 #end if
243
244
245 #if $plot_type.pt_size
246 --pt-size '$plot_type.pt_size'
247 #end if
248
249 $plot_type.order
250
251
252 #if $plot_type.min_cutoff
253 --min-cutoff '$plot_type.min_cutoff'
254 #end if
255
256
257 #if $plot_type.max_cutoff
258 --max-cutoff '$plot_type.max_cutoff'
259 #end if
260
261
262 #if $plot_type.reduction
263 --reduction '$plot_type.reduction'
264 #end if
265
266
267 #if $plot_type.split_by
268 --split-by '$plot_type.split_by'
269 #end if
270
271
272 --keep-scale '$plot_type.keep_scale'
273
274
275 #if $plot_type.shape_by
276 --shape-by '$plot_type.shape_by'
277 #end if
278
279
280 #if $plot_type.slot
281 --slot '$plot_type.slot'
282 #end if
283
284 $plot_type.blend
285
286
287 #if $plot_type.blend_threshold
288 --blend-threshold '$plot_type.blend_threshold'
289 #end if
290
291 $plot_type.label
292
293
294 #if $plot_type.label_size
295 --label-size '$plot_type.label_size'
296 #end if
297
298 $plot_type.repel
299
300
301 #if $plot_type.ncol
302 --ncol '$plot_type.ncol'
303 #end if
304
305 $plot_type.coord_fixed
306
307 $plot_type.by_col
308
309 #elif str($plot_type.plot_type_selector) == 'VlnPlot':
310
311 --features '$plot_type.features'
312
313
314 #if $plot_type.cols
315 --cols '$plot_type.cols'
316 #end if
317
318
319 #if $plot_type.pt_size
320 --pt-size '$plot_type.pt_size'
321 #end if
322
323
324 #if $plot_type.idents
325 --idents '$plot_type.idents'
326 #end if
327
328 $plot_type.sort
329
330
331 #if $plot_type.assay
332 --assay '$plot_type.assay'
333 #end if
334
335
336 #if $plot_type.group_by
337 --group-by '$plot_type.group_by'
338 #end if
339
340
341 #if $plot_type.split_by
342 --split-by '$plot_type.split_by'
343 #end if
344
345
346 #if $plot_type.adjust
347 --adjust '$plot_type.adjust'
348 #end if
349
350 $plot_type.same_y_lims
351
352 $plot_type.log
353
354
355 #if $plot_type.ncol
356 --ncol '$plot_type.ncol'
357 #end if
358
359
360 #if $plot_type.slot
361 --slot '$plot_type.slot'
362 #end if
363
364 $plot_type.split_plot
365
366 $plot_type.stack
367
368
369 #if $plot_type.fill_by
370 --fill-by '$plot_type.fill_by'
371 #end if
372
373 $plot_type.flip
374
375 #elif str($plot_type.plot_type_selector) == 'DotPlot':
376
377 #if $plot_type.assay
378 --assay '$plot_type.assay'
379 #end if
380
381
382 --features '$plot_type.features'
383
384
385 #if $plot_type.cols_dot_plot
386 --cols-dot-plot '$plot_type.cols_dot_plot'
387 #end if
388
389
390 #if $plot_type.col_min
391 --col-min '$plot_type.col_min'
392 #end if
393
394
395 #if $plot_type.col_max
396 --col-max '$plot_type.col_max'
397 #end if
398
399
400 #if $plot_type.dot_min
401 --dot-min '$plot_type.dot_min'
402 #end if
403
404
405 #if $plot_type.dot_scale
406 --dot-scale '$plot_type.dot_scale'
407 #end if
408
409
410 #if $plot_type.idents
411 --idents '$plot_type.idents'
412 #end if
413
414
415 #if $plot_type.group_by
416 --group-by '$plot_type.group_by'
417 #end if
418
419
420 #if $plot_type.split_by
421 --split-by '$plot_type.split_by'
422 #end if
423
424 $plot_type.cluster_idents
425
426 $plot_type.scale
427
428
429 #if $plot_type.scale_by
430 --scale-by '$plot_type.scale_by'
431 #end if
432
433 #end if
434
435
436 #if $enable_output_rds_file
437 --output-rds-file '$output_rds_file'
438 #end if
439
440
441 --plot-format '$plot_format'
442
443
444 --units '$units'
445
446
447 --dpi '$dpi'
448
449 $limitsize
450
451
452 #if $bg
453 --bg '$bg'
454 #end if
455
456
457
458 ]]></command>
459 <inputs>
460 <expand macro="input_object_params" />
461 <conditional name="plot_type">
462 <param label="Plot_type_selector" name="plot_type_selector" argument="--plot_type_selector" type="select" help="Either FeaturePlot, RidgePlot, DimPlot, VlnPlot or DotPlot.">
463 <option value="DimPlot">DimPlot</option>
464 <option value="DoHeatmap">DoHeatmap</option>
465 <option value="RidgePlot">RidgePlot</option>
466 <option value="FeaturePlot" selected="true">FeaturePlot</option>
467 <option value="VlnPlot">VlnPlot</option>
468 <option value="DotPlot">DotPlot</option>
469 </param>
470 <when value="DimPlot">
471 <param label="Dims" optional='true' value='1,2' name="dims" argument="--dims" type="text" help="Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions"/>
472 <param label="Cells" optional='true' name="cells" argument="--cells" type="text" help="Vector of cells to plot (default is all cells)"/>
473 <param label="Cols" optional='true' name="cols" argument="--cols" type="text" help="Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info. By default, ggplot2 assigns colors. We also include a number of palettes from the pals package. See 'DiscretePalette' for details."/>
474 <param label="Pt size" optional='true' name="pt_size" argument="--pt-size" type="integer" help="Adjust point size for plotting"/>
475 <param label="Reduction" optional='true' name="reduction" argument="--reduction" type="text" help="Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca"/>
476 <param label="Group by" optional='true' name="group_by" argument="--group-by" type="text" help="Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class"/>
477 <param label="Split by" optional='true' name="split_by" argument="--split-by" type="text" help="Name of a metadata column to split plot by; see 'FetchData' for more details"/>
478 <param label="Shape by" optional='true' name="shape_by" argument="--shape-by" type="text" help="If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells. Only applicable if raster is FALSE."/>
479 <param label="Order" optional='true' name="order" argument="--order" type="text" help="Specify the order of plotting for the idents. This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top)"/>
480 <param label="Shuffle" optional='true' value='false' name="shuffle" argument="--shuffle" type="boolean" truevalue='--shuffle' falsevalue='' checked='false' help="Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (default is FALSE)"/>
481 <param label="Seed" optional='true' value='1' name="seed" argument="--seed" type="integer" help="Sets the seed if randomly shuffling the order of points."/>
482 <param label="Label" optional='true' value='false' name="label" argument="--label" type="boolean" truevalue='--label' falsevalue='' checked='false' help="Whether to label the clusters"/>
483 <param label="Label size" optional='true' value='4' name="label_size" argument="--label-size" type="integer" help="Sets size of labels"/>
484 <param label="Label color" optional='true' value='black' name="label_color" argument="--label-color" type="text" help="Sets the color of the label text"/>
485 <param label="Label box" optional='true' value='false' name="label_box" argument="--label-box" type="boolean" truevalue='--label-box' falsevalue='' checked='false' help="Whether to put a box around the label text (geom_text vs geom_label)"/>
486 <param label="Repel" optional='true' value='false' name="repel" argument="--repel" type="boolean" truevalue='--repel' falsevalue='' checked='false' help="Repel labels"/>
487 <param label="Cells highlight" optional='true' name="cells_highlight" argument="--cells-highlight" type="text" help="A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in 'cols.highlight' and other cells black (white if dark.theme = TRUE); will also resize to the size(s) passed to 'sizes.highlight'."/>
488 <param label="Cols highlight" optional='true' value='#DE2D26' name="cols_highlight" argument="--cols-highlight" type="text" help="A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight. Comma separated."/>
489 <param label="Sizes highlight" optional='true' value='1' name="sizes_highlight" argument="--sizes-highlight" type="integer" help="Size of highlighted cells; will repeat to the length groups in cells.highlight"/>
490 <param label="Na value" optional='true' value='grey50' name="na_value" argument="--na-value" type="text" help="Color value for NA points when using custom scale"/>
491 <param label="Ncol" optional='true' name="ncol" argument="--ncol" type="integer" help="Number of columns for display when combining plots"/>
492 </when>
493 <when value="DoHeatmap">
494 <param label="Features" optional='true' name="features" argument="--features" type="text" help="A vector of features to plot, defaults to VariableFeatures of the object."/>
495 <param label="Cells" optional='true' name="cells" argument="--cells" type="text" help="A vector of cells to plot, comma separated"/>
496 <param label="Group by" optional='true' value='ident' name="group_by" argument="--group-by" type="text" help="A vector of variables to group cells by; pass 'ident' to group by cell identity classes"/>
497 <param label="Group bar" optional='true' value='true' name="group_bar" argument="--do-not-group-bar" type="boolean" truevalue='' falsevalue='--do-not-group-bar' checked='true' help="Add a color bar showing group status for cells"/>
498 <param label="Group colors" optional='true' name="group_colors" argument="--group-colors" type="text" help="Colors to use for the color bar, comma separated."/>
499 <param label="Disp min" optional='true' value='-2' name="disp_min" argument="--disp-min" type="integer" help="Minimum display value (all values below are clipped)"/>
500 <param label="Disp max" optional='true' name="disp_max" argument="--disp-max" type="integer" help="Maximum display value (all values above are clipped); defaults to 2.5 if slot is 'scale.data', 6 otherwise"/>
501 <param label="Slot" name="slot" argument="--slot" type="select" help="Data slot to use, choose from raw.data, data, or scale.data">
502 <option value="scale.data" selected="true">Scale data</option>
503 <option value="data">Data</option>
504 <option value="raw.data">Raw data</option>
505 </param>
506 <param label="Assay" optional='true' name="assay" argument="--assay" type="text" help="Assay to pull from"/>
507 <param label="Label" optional='true' value='true' name="label" argument="--do-not-label" type="boolean" truevalue='' falsevalue='--do-not-label' checked='true' help="Label the cell identies above the color bar"/>
508 <param label="Size" optional='true' value='5' name="size" argument="--size" type="integer" help="Size of text above color bar"/>
509 <param label="Hjust" optional='true' value='0' name="hjust" argument="--hjust" type="integer" help="Horizontal justification of text above color bar"/>
510 <param label="Angle" optional='true' value='45' name="angle" argument="--angle" type="integer" help="Angle of text above color bar"/>
511 <param label="Raster" optional='true' value='true' name="raster" argument="--do-not-raster" type="boolean" truevalue='' falsevalue='--do-not-raster' checked='true' help="If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render)."/>
512 <param label="Draw lines" optional='true' value='true' name="draw_lines" argument="--do-not-draw-lines" type="boolean" truevalue='' falsevalue='--do-not-draw-lines' checked='true' help="Include white lines to separate the groups"/>
513 <param label="Lines width" optional='true' name="lines_width" argument="--lines-width" type="integer" help="Integer number to adjust the width of the separating white lines. Corresponds to the number of cells between each group."/>
514 <param label="Group bar height" optional='true' value='0' name="group_bar_height" argument="--group-bar-height" type="integer" help="Scale the height of the color bar"/>
515 <param label="Combine" optional='true' value='true' name="combine" argument="--do-not-combine" type="boolean" truevalue='' falsevalue='--do-not-combine' checked='true' help="Combine plots into a single patchwork or ed ggplot object. If FALSE return a list of ggplot objects."/>
516 </when>
517 <when value="RidgePlot">
518 <param label="Features" optional='true' value='' name="features" argument="--features" type="text" help="Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)"/>
519 <param label="Cols-ridgeplot" optional='true' name="cols_ridgeplot" argument="--cols-ridgeplot" type="text" help="Colors to use for plotting, comma separated"/>
520 <param label="Idents" optional='true' name="idents" argument="--idents" type="text" help="Which classes to include in the plot (default is all)"/>
521 <param label="Sort" optional='true' value='false' name="sort" argument="--sort" type="boolean" truevalue='--sort' falsevalue='' checked='false' help="Sort identity classes (on the x-axis) by the average expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction"/>
522 <param label="Assay" optional='true' name="assay" argument="--assay" type="text" help="Name of assay to use, defaults to the active assay"/>
523 <param label="Group by" optional='true' name="group_by" argument="--group-by" type="text" help="Group (color) cells in different ways (for example, orig.ident)"/>
524 <param label="Same y lims" optional='true' value='false' name="same_y_lims" argument="--same-y-lims" type="boolean" truevalue='--same-y-lims' falsevalue='' checked='false' help="Set all the y-axis limits to the same values"/>
525 <param label="Log" optional='true' value='false' name="log" argument="--log" type="boolean" truevalue='--log' falsevalue='' checked='false' help="plot the feature axis on log scale"/>
526 <param label="Ncol" optional='true' name="ncol" argument="--ncol" type="integer" help="Number of columns if multiple plots are displayed"/>
527 <param label="Slot" optional='true' value='data' name="slot" argument="--slot" type="text" help="Use non-normalized counts data for plotting"/>
528 <param label="Stack" optional='true' value='false' name="stack" argument="--stack" type="boolean" truevalue='--stack' falsevalue='' checked='false' help="Horizontally stack plots for each feature"/>
529 <param label="Fill by" optional='true' value='feature' name="fill_by" argument="--fill-by" type="text" help="Color violins/ridges based on either 'feature' or 'ident'"/>
530 </when>
531 <when value="FeaturePlot">
532 <param label="Features" name="features" argument="--features" type="text" help="Vector of features to plot. Features can come from: an assay feature (e.g. a gene name - MS4A1), a column name from meta.data (e.g. mitochondrial percentage - percent.mito), a column name from a DimReduc object corresponding to the cell embedding values (e.g. the PC 1 scores - PC_1)."/>
533 <param label="Dims" optional='true' value='1,2' name="dims" argument="--dims" type="text" help="Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions"/>
534 <param label="Cells" optional='true' name="cells" argument="--cells" type="text" help="Vector of cells to plot (default is all cells)"/>
535 <param label="Cols-feature-plot" optional='true' value='lightgrey,blue' name="cols_feature_plot" argument="--cols-feature-plot" type="text" help="The two colors to form the gradient over. Provide as string vector with the first color corresponding to low values, the second to high. Also accepts a Brewer color scale or vector of colors."/>
536 <param label="Pt size" optional='true' name="pt_size" argument="--pt-size" type="integer" help="Adjust point size for plotting"/>
537 <param label="Order" optional='true' value='false' name="order" argument="--order" type="boolean" truevalue='--order' falsevalue='' checked='false' help="Boolean determining whether to plot cells in order of expression. Can be useful if cells expressing given feature are getting buried."/>
538 <param label="Min cutoff" optional='true' name="min_cutoff" argument="--min-cutoff" type="text" help="Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')"/>
539 <param label="Max cutoff" optional='true' name="max_cutoff" argument="--max-cutoff" type="text" help="Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')"/>
540 <param label="Reduction" optional='true' name="reduction" argument="--reduction" type="text" help="Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca"/>
541 <param label="Split by" optional='true' name="split_by" argument="--split-by" type="text" help="A factor in object metadata to split the feature plot by, pass ident to split by cell identity; similar to the old FeatureHeatmap."/>
542 <param label="Keep scale" name="keep_scale" argument="--keep-scale" type="select" help="How to handle the color scale across multiple plots.">
543 <option value="feature" selected="true">By row/feature scaling: The plots for each individual feature are scaled to the maximum expression of the feature across the conditions provided to 'split.by'.</option>
544 <option value="all">Universal scaling: The plots for all features and conditions are scaled to the maximum expression value for the feature with the highest overall expression.</option>
545 <option value="None">No scaling: Each individual plot is scaled to the maximum expression value of the feature in the condition provided to 'split.by'. Be aware setting NULL will result in color scales that are not comparable between plots.</option>
546 </param>
547 <param label="Shape by" optional='true' name="shape_by" argument="--shape-by" type="text" help="If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells. Only applicable if 'raster' is FALSE) ."/>
548 <param label="Slot" optional='true' value='data' name="slot" argument="--slot" type="text" help="Which slot to pull expression data from?"/>
549 <param label="Blend" optional='true' value='false' name="blend" argument="--blend" type="boolean" truevalue='--blend' falsevalue='' checked='false' help="Scale and blend expression values to visualize coexpression of two features"/>
550 <param label="Blend threshold" optional='true' value='0' name="blend_threshold" argument="--blend-threshold" type="integer" help="The color cutoff from weak signal to strong signal; ranges from 0 to 1."/>
551 <param label="Label" optional='true' value='false' name="label" argument="--label" type="boolean" truevalue='--label' falsevalue='' checked='false' help="Whether to label the clusters"/>
552 <param label="Label size" optional='true' value='4' name="label_size" argument="--label-size" type="integer" help="Sets size of labels"/>
553 <param label="Repel" optional='true' value='false' name="repel" argument="--repel" type="boolean" truevalue='--repel' falsevalue='' checked='false' help="Repel labels"/>
554 <param label="Ncol" optional='true' name="ncol" argument="--ncol" type="integer" help="Number of columns to combine multiple feature plots to, ignored if split.by is not NULL"/>
555 <param label="Coord fixed" optional='true' value='false' name="coord_fixed" argument="--coord-fixed" type="boolean" truevalue='--coord-fixed' falsevalue='' checked='false' help="Plot cartesian coordinates with fixed aspect ratio"/>
556 <param label="By col" optional='true' value='true' name="by_col" argument="--do-not-by-col" type="boolean" truevalue='' falsevalue='--do-not-by-col' checked='true' help="If splitting by a factor, plot the splits per column with the features as rows; ignored if blend = TRUE."/>
557 </when>
558 <when value="VlnPlot">
559 <param label="Features" optional='true' value='' name="features" argument="--features" type="text" help="Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)"/>
560 <param label="Cols" optional='true' name="cols" argument="--cols" type="text" help="Colors to use for plotting, comma separated."/>
561 <param label="Pt size" optional='true' name="pt_size" argument="--pt-size" type="integer" help="Point size for geom_violin"/>
562 <param label="Idents" optional='true' name="idents" argument="--idents" type="text" help="Which classes to include in the plot (default is all)"/>
563 <param label="Sort" optional='true' value='false' name="sort" argument="--sort" type="boolean" truevalue='--sort' falsevalue='' checked='false' help="Sort identity classes (on the x-axis) by the average expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction"/>
564 <param label="Assay" optional='true' name="assay" argument="--assay" type="text" help="Name of assay to use, defaults to the active assay"/>
565 <param label="Group by" optional='true' name="group_by" argument="--group-by" type="text" help="Group (color) cells in different ways (for example, orig.ident)"/>
566 <param label="Split by" optional='true' name="split_by" argument="--split-by" type="text" help="A variable to split the violin plots by,"/>
567 <param label="Adjust" optional='true' value='1' name="adjust" argument="--adjust" type="integer" help="Adjust parameter for geom_violin"/>
568 <param label="Same y lims" optional='true' value='false' name="same_y_lims" argument="--same-y-lims" type="boolean" truevalue='--same-y-lims' falsevalue='' checked='false' help="Set all the y-axis limits to the same values"/>
569 <param label="Log" optional='true' value='false' name="log" argument="--log" type="boolean" truevalue='--log' falsevalue='' checked='false' help="plot the feature axis on log scale"/>
570 <param label="Ncol" optional='true' name="ncol" argument="--ncol" type="integer" help="Number of columns if multiple plots are displayed"/>
571 <param label="Slot" optional='true' value='data' name="slot" argument="--slot" type="text" help="Use non-normalized counts data for plotting"/>
572 <param label="Split plot" optional='true' value='false' name="split_plot" argument="--split-plot" type="boolean" truevalue='--split-plot' falsevalue='' checked='false' help="plot each group of the split violin plots by multiple or single violin shapes."/>
573 <param label="Stack" optional='true' value='false' name="stack" argument="--stack" type="boolean" truevalue='--stack' falsevalue='' checked='false' help="Horizontally stack plots for each feature"/>
574 <param label="Fill by" optional='true' value='feature' name="fill_by" argument="--fill-by" type="text" help="Color violins/ridges based on either 'feature' or 'ident'"/>
575 <param label="Flip" optional='true' value='false' name="flip" argument="--flip" type="boolean" truevalue='--flip' falsevalue='' checked='false' help="flip plot orientation (identities on x-axis)"/>
576 </when>
577 <when value="DotPlot">
578 <param label="Assay" optional='true' name="assay" argument="--assay" type="text" help="Name of assay to use, defaults to the active assay"/>
579 <param label="Features" optional='true' value='' name="features" argument="--features" type="text" help="Input vector of features, or named list of feature vectors if feature-grouped panels are desired (replicates the functionality of the old SplitDotPlotGG)"/>
580 <param label="Cols-dot-plot" optional='true' value='yellow,lightgrey,blue' name="cols_dot_plot" argument="--cols-dot-plot" type="text" help="Colors to plot: the name of a palette from RColorBrewer::brewer.pal.info , a pair of colors defining a gradient, or 3+ colors defining multiple gradients (if split.by is set)"/>
581 <param label="Col min" optional='true' value='-2' name="col_min" argument="--col-min" type="integer" help="Minimum scaled average expression threshold (everything smaller will be set to this)"/>
582 <param label="Col max" optional='true' value='2' name="col_max" argument="--col-max" type="integer" help="Maximum scaled average expression threshold (everything larger will be set to this)"/>
583 <param label="Dot min" optional='true' value='0' name="dot_min" argument="--dot-min" type="integer" help="The fraction of cells at which to draw the smallest dot (default is 0). All cell groups with less than this expressing the given gene will have no dot drawn."/>
584 <param label="Dot scale" optional='true' value='6' name="dot_scale" argument="--dot-scale" type="integer" help="Scale the size of the points, similar to cex"/>
585 <param label="Idents" optional='true' name="idents" argument="--idents" type="text" help="Identity classes to include in plot (default is all)"/>
586 <param label="Group by" optional='true' name="group_by" argument="--group-by" type="text" help="Factor to group the cells by"/>
587 <param label="Split by" optional='true' name="split_by" argument="--split-by" type="text" help="Factor to split the groups by (replicates the functionality of the old SplitDotPlotGG); see 'FetchData' for more details."/>
588 <param label="Cluster idents" optional='true' value='false' name="cluster_idents" argument="--cluster-idents" type="boolean" truevalue='--cluster-idents' falsevalue='' checked='false' help="Whether to order identities by hierarchical clusters based on given features, default is FALSE"/>
589 <param label="Scale" optional='true' value='true' name="scale" argument="--do-not-scale" type="boolean" truevalue='' falsevalue='--do-not-scale' checked='true' help="Determine whether the data is scaled, will be done by default"/>
590 <param label="Scale by" name="scale_by" argument="--scale-by" type="select" help="Scale the size of the points by 'size' or by 'radius'">
591 <option value="size">Size</option>
592 <option value="radius" selected="true">Radius</option>
593 </param>
594 </when>
595 </conditional>
596 <param label="Plot-format" name="plot_format" argument="--plot-format" type="select" help="Format to use, either PNG, EPS, PostScript, TeX, PDF, JPEG, TIFF or SVG">
597 <option value="png" selected="true">PNG</option>
598 <option value="eps">EPS</option>
599 <option value="ps">PostScript</option>
600 <option value="tex">TeX (pictex)</option>
601 <option value="pdf">PDF</option>
602 <option value="jpg">JPG</option>
603 <option value="tiff">TIFF</option>
604 <option value="svg">SVG</option>
605 </param>
606 <param label="Units" name="units" argument="--units" type="select" help="Units for the plot dimensions.">
607 <option value="cm" selected="true">Centimeters</option>
608 <option value="in">Inches</option>
609 <option value="mm">Milimeters</option>
610 <option value="px">Pixels</option>
611 </param>
612 <param label="Dpi" name="dpi" argument="--dpi" type="select" help="Plot resolution. Also accepts a string input: retina (320), print (300), or screen (72). Applies only to raster output types.">
613 <option value="320">Retina</option>
614 <option value="300" selected="true">Print</option>
615 <option value="72">screen</option>
616 </param>
617 <param label="Limitsize" optional='true' value='true' name="limitsize" argument="--do-not-limitsize" type="boolean" truevalue='' falsevalue='--do-not-limitsize' checked='true' help="When TRUE (the default) ggsave() will not save images larger than 50x50 inches, to prevent the common error of specifying dimensions in pixels."/>
618 <param label="Bg" optional='true' name="bg" argument="--bg" type="text" help="Background colour. If NULL, uses the plot.background fill value from the plot theme."/>
619 <param label="Enable_output_rds_file" optional='true' value='false' name="enable_output_rds_file" argument="--enable_output_rds_file" type="boolean" truevalue='--enable_output_rds_file' falsevalue='' checked='false' help="Enable output output_rds_file"/>
620
621 </inputs>
622 <outputs>
623 <expand macro="plot_output_files_format" format="png" />
624 <expand macro="plot_output_files_format" format="pdf" />
625 <expand macro="plot_output_files_format" format="eps" />
626 <expand macro="plot_output_files_format" format="jpg" />
627 <expand macro="plot_output_files_format" format="ps" />
628 <expand macro="plot_output_files_format" format="tiff" />
629 <expand macro="plot_output_files_format" format="svg" />
630
631 <data label="${tool.name} on ${on_string}: Output-rds-file" name="output_rds_file" format='?'>
632 <filter>enable_output_rds_file</filter>
633 </data>
634 </outputs>
635 <tests>
636 <!-- MANUAL TESTS -->
637 <test>
638 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
639 <param name="plot_type_selector" value="FeaturePlot"/>
640 <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>
641 <output name="plot_out_png" ftype="png" >
642 <assert_contents>
643 <has_size value="195414" delta="32000"/>
644 </assert_contents>
645 </output>
646 </test>
647 <test>
648 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
649 <param name="plot_type_selector" value="VlnPlot"/>
650 <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>
651 <param name="plot_format" value="pdf"/>
652 <output name="plot_out_pdf" ftype="pdf" >
653 <assert_contents>
654 <has_size value="1239200" delta="123000"/>
655 </assert_contents>
656 </output>
657 </test>
658 <test>
659 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
660 <param name="plot_type_selector" value="RidgePlot"/>
661 <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>
662 <param name="plot_format" value="eps"/>
663 <output name="plot_out_eps" ftype="eps" >
664 <assert_contents>
665 <has_size value="84892" delta="8400"/>
666 </assert_contents>
667 </output>
668 </test>
669 <test>
670 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
671 <param name="plot_type_selector" value="DotPlot"/>
672 <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>
673 <param name="plot_format" value="ps"/>
674 <output name="plot_out_ps" ftype="ps" >
675 <assert_contents>
676 <has_size value="16615" delta="1600"/>
677 </assert_contents>
678 </output>
679 </test>
680 <test>
681 <param name="rds_seurat_file" ftype="rdata" value="UMAP_result_integrated.rds"/>
682 <param name="plot_type_selector" value="DoHeatmap"/>
683 <param name="features" value="GPC5-AS1,MAFB,FAP,PPY"/>
684 <output name="plot_out_png" ftype="png" >
685 <assert_contents>
686 <has_size value="83227" delta="8600"/>
687 </assert_contents>
688 </output>
689 </test>
690 <!-- END MANUAL TESTS -->
691 </tests>
692 <help>
693 <!-- MANUAL HELP -->
694 <![CDATA[
695 .. class:: infomark
696
697 **What it does**
698
699 @SEURAT_INTRO@
700
701 This tool produces the different plots available on Seurat.
702
703 -----
704
705 **Inputs**
706
707 * Seurat object or compatible (can be specified in different formats)
708 * Plot type (can be specified in different formats)
709 * Potential compulsory options for each plot type
710
711 All the rest of the parameters are optional.
712
713 -----
714
715 **Outputs**
716
717 * A plot in the specified format
718 * Optionally, an RDS object with the ggplo2 plot.
719
720 @VERSION_HISTORY@
721
722 ]]>
723 <!-- END MANUAL HELP -->
724 </help>
725 <expand macro="citations" />
726 </tool>