Mercurial > repos > ebi-gxa > seurat_dim_plot

annotate seurat_dim_plot.xml @ 0:6e26ee99fdfc draft

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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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children daeca8f7a26e
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6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0">
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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7 <expand macro="version" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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8 <command detect_errors="exit_code"><![CDATA[
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 seurat-dim-plot.R
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 --input-object-file '$input'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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14 #if $dim_1
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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15 --dim-1 $dim_1
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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16 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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17 #if $dim_2
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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26 #if $label_size
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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29 --do-label $do_label
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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30 #if $group_by
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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31 --group-by $group_by
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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32 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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33 #if $plot_title
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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34 --plot-title '$plot_title'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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35 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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36 --do-bare $do_bare
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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37 #if $cols_use
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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38 --cols-use '$cols_use'
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
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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40 #if $pt_shape
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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41 --pt-shape '$pt_shape'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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42 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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43 --coord-fixed $coord_fixed
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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44 --no-axes $no_axes
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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45 --dark-theme $dark_theme
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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46 #if $plot_order
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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47 --plot-order '$plot_order'
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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48 #end if
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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49 --png-width $png_width
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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50 --png-height $png_height
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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51 --output-image-file $output_image_file
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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52 ]]></command>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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53 <inputs>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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54 <param type="data" name="input" format="rdata" label="RDS object" help='File in which a serialized R matrix object may be found'/>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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56 <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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57 <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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'/>
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="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
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="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
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="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
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62 <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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63 <param type="text" name="plot_title" format="text" label='Plot title' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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64 <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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.' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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.' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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68 <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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69 <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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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).' />
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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71 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width 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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72 <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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73 </inputs>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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74 <outputs>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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75 <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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76 </outputs>
6e26ee99fdfc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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77 <tests>
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78 <test>
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79 <param name="input" value="seurat_clustered.rds" />
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80 <output name="output_image_file" file="pca.png" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 .. class:: infomark
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85
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86 **What it does**
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87
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88 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing
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89 data. It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to
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90 identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to
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91 integrate diverse types of single cell data.
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92
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93 This tool graphs the output of a dimensional reduction technique (PCA by default). Cells are colored
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94 by their identity class.
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95
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96 -----
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97
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98 **Inputs**
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99
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100 * Seurat RDS object
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101
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102 -----
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103
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104 **Outputs**
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105
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106 * PNG-format image file
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107
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108 .. _Seurat: https://www.nature.com/articles/nbt.4096
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109 .. _Satija Lab: https://satijalab.org/seurat/
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110
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111 @VERSION_HISTORY@
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112
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113 ]]></help>
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114 <expand macro="citations" />
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115 </tool>