Mercurial > repos > ebi-gxa > seurat_dim_plot

annotate 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
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5
316623eb59bd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
0
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2 <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <macros>
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4 <import>seurat_macros.xml</import>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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5 </macros>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 seurat-dim-plot.R
1
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10 @INPUT_OBJECT@
0
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11 #if $reduction_use
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12 --reduction-use '$reduction_use'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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13 #end if
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14 #if $dim_1
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15 --dim-1 $dim_1
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16 #end if
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17 #if $dim_2
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18 --dim-2 $dim_2
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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19 #end if
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20 #if $cells_use
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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21 --cells-use $cells_use
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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22 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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23 #if $pt_size
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24 --pt-size $pt_size
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 #end if
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26 #if $label_size
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27 --label-size $label_size
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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28 #end if
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29 --do-label $do_label
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30 --repel $repel
0
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31 #if $group_by
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32 --group-by $group_by
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33 #end if
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34 #if $cols_use
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35 --cols-use '$cols_use'
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36 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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37 #if $pt_shape
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38 --pt-shape '$pt_shape'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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39 #end if
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40 #if $plot_order
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41 --plot-order '$plot_order'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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42 #end if
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43 --png-width $png_width
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44 --png-height $png_height
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45 --output-image-file $output_image_file
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46 ]]></command>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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47 <inputs>
1
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48 <expand macro="input_object_params"/>
0
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49 <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' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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50 <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' />
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51 <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' />
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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'/>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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53 <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
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54 <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
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55 <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
5
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56 <param type="boolean" name="repel" checked="false" label='Repel labels' truevalue="TRUE" falsevalue="FALSE" />
0
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57 <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
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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.' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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.' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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).' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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61 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
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62 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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63 </inputs>
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64 <outputs>
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65 <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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66 </outputs>
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67 <tests>
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68 <test>
5
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69 <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells-tsne.rds" ftype="rdata" />
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70 <output name="output_image_file" >
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71 <assert_contents>
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72 <has_size value="18122" delta="2000"/>
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73 </assert_contents>
316623eb59bd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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74 </output>
0
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75 </test>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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76 </tests>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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77 <help><![CDATA[
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78 .. class:: infomark
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79
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80 **What it does**
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81
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82 Graphs the output of a dimensional reduction technique on a 2D scatter plot
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83 where each point is a cell and it's positioned based on the cell embeddings
daeca8f7a26e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
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84 determined by the reduction technique. By default, cells are colored by their
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85 identity class (can be changed with the group.by parameter).
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86
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87 @SEURAT_INTRO@
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88
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89 -----
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90
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91 **Inputs**
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92
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93 * Seurat RDS object
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94
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95 -----
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96
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97 **Outputs**
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98
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99 * PNG-format image file
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100
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101 .. _Seurat: https://www.nature.com/articles/nbt.4096
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102 .. _Satija Lab: https://satijalab.org/seurat/
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103
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104 @VERSION_HISTORY@
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105
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106 ]]></help>
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107 <expand macro="citations" />
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108 </tool>