Mercurial > repos > ebi-gxa > seurat_dim_plot

comparison seurat_dim_plot.xml @ 5:316623eb59bd draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:25:13 +0000
parents cfc3d8ee3a64
children 64174ac50d78
comparison
equal deleted inserted replaced
4:cfc3d8ee3a64 5:316623eb59bd
1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="@SEURAT_VERSION@+galaxy0"> 1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
2 <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description> 2 <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
3 <macros> 3 <macros>
4 <import>seurat_macros.xml</import> 4 <import>seurat_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
25 #end if 25 #end if
26 #if $label_size 26 #if $label_size
27 --label-size $label_size 27 --label-size $label_size
28 #end if 28 #end if
29 --do-label $do_label 29 --do-label $do_label
30 --repel $repel
30 #if $group_by 31 #if $group_by
31 --group-by $group_by 32 --group-by $group_by
32 #end if 33 #end if
33 #if $plot_title
34 --plot-title '$plot_title'
35 #end if
36 --do-bare $do_bare
37 #if $cols_use 34 #if $cols_use
38 --cols-use '$cols_use' 35 --cols-use '$cols_use'
39 #end if 36 #end if
40 #if $pt_shape 37 #if $pt_shape
41 --pt-shape '$pt_shape' 38 --pt-shape '$pt_shape'
42 #end if 39 #end if
43 --coord-fixed $coord_fixed
44 --no-axes $no_axes
45 --dark-theme $dark_theme
46 #if $plot_order 40 #if $plot_order
47 --plot-order '$plot_order' 41 --plot-order '$plot_order'
48 #end if 42 #end if
49 --png-width $png_width 43 --png-width $png_width
50 --png-height $png_height 44 --png-height $png_height
57 <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' /> 51 <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'/> 52 <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' /> 53 <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'/> 54 <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" /> 55 <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
56 <param type="boolean" name="repel" checked="false" label='Repel labels' truevalue="TRUE" falsevalue="FALSE" />
62 <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' /> 57 <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.' /> 58 <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.' /> 59 <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).' /> 60 <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.' /> 61 <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.'/> 62 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
73 </inputs> 63 </inputs>
74 <outputs> 64 <outputs>
75 <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/> 65 <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
76 </outputs> 66 </outputs>
77 <tests> 67 <tests>
78 <test> 68 <test>
79 <param name="rds_seurat_file" value="cluster_seurat.rds" ftype="rdata" /> 69 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells-tsne.rds" ftype="rdata" />
80 <param name="do_bare" value="True" /> 70 <output name="output_image_file" >
81 <output name="output_image_file" file="pcatest.png" compare="sim_size" delta="5000000" /> 71 <assert_contents>
72 <has_size value="18122" delta="2000"/>
73 </assert_contents>
74 </output>
82 </test> 75 </test>
83 </tests> 76 </tests>
84 <help><![CDATA[ 77 <help><![CDATA[
85 .. class:: infomark 78 .. class:: infomark
86 79