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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:20:03 -0400
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1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0">
2 <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</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 seurat-dim-plot.R
10 --input-object-file '$input'
11 #if $reduction_use
12 --reduction-use '$reduction_use'
13 #end if
14 #if $dim_1
15 --dim-1 $dim_1
16 #end if
17 #if $dim_2
18 --dim-2 $dim_2
19 #end if
20 #if $cells_use
21 --cells-use $cells_use
22 #end if
23 #if $pt_size
24 --pt-size $pt_size
25 #end if
26 #if $label_size
27 --label-size $label_size
28 #end if
29 --do-label $do_label
30 #if $group_by
31 --group-by $group_by
32 #end if
33 #if $plot_title
34 --plot-title '$plot_title'
35 #end if
36 --do-bare $do_bare
37 #if $cols_use
38 --cols-use '$cols_use'
39 #end if
40 #if $pt_shape
41 --pt-shape '$pt_shape'
42 #end if
43 --coord-fixed $coord_fixed
44 --no-axes $no_axes
45 --dark-theme $dark_theme
46 #if $plot_order
47 --plot-order '$plot_order'
48 #end if
49 --png-width $png_width
50 --png-height $png_height
51 --output-image-file $output_image_file
52 ]]></command>
53 <inputs>
54 <param type="data" name="input" format="rdata" label="RDS object" help='File in which a serialized R matrix object may be found'/>
55 <param type="text" name="reduction_use" value='pca' label="Dimensionality reduction" help='Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed' />
56 <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' />
57 <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' />
58 <param type="data" name="cells_use" format="tabular" label="Cells list" help='File to be used to derive a vector of cells to plot (default is all cells)' optional='true'/>
59 <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
60 <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
61 <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
62 <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
63 <param type="text" name="plot_title" format="text" label='Plot title' />
64 <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
65 <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
66 <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" 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.' />
67 <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
68 <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
69 <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
70 <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). 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).' />
71 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
72 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
73 </inputs>
74 <outputs>
75 <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
76 </outputs>
77 <tests>
78 <test>
79 <param name="input" value="seurat_clustered.rds" />
80 <output name="output_image_file" file="pca.png" />
81 </test>
82 </tests>
83 <help><![CDATA[
84 .. class:: infomark
85
86 **What it does**
87
88 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing
89 data. It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to
90 identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to
91 integrate diverse types of single cell data.
92
93 This tool graphs the output of a dimensional reduction technique (PCA by default). Cells are colored
94 by their identity class.
95
96 -----
97
98 **Inputs**
99
100 * Seurat RDS object
101
102 -----
103
104 **Outputs**
105
106 * PNG-format image file
107
108 .. _Seurat: https://www.nature.com/articles/nbt.4096
109 .. _Satija Lab: https://satijalab.org/seurat/
110
111 @VERSION_HISTORY@
112
113 ]]></help>
114 <expand macro="citations" />
115 </tool>