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author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:40:27 +0000 |
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<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description> <macros> <import>seurat_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version" /> <command detect_errors="exit_code"><![CDATA[ seurat-dim-plot.R @INPUT_OBJECT@ #if $reduction_use --reduction-use '$reduction_use' #end if #if $dim_1 --dim-1 $dim_1 #end if #if $dim_2 --dim-2 $dim_2 #end if #if $cells_use --cells-use $cells_use #end if #if $pt_size --pt-size $pt_size #end if #if $label_size --label-size $label_size #end if --do-label $do_label --repel $repel #if $group_by --group-by $group_by #end if #if $cols_use --cols-use '$cols_use' #end if #if $pt_shape --pt-shape '$pt_shape' #end if #if $plot_order --plot-order '$plot_order' #end if --png-width $png_width --png-height $png_height --output-image-file $output_image_file ]]></command> <inputs> <expand macro="input_object_params"/> <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' /> <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' /> <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' /> <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'/> <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' /> <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/> <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" /> <param type="boolean" name="repel" checked="false" label='Repel labels' truevalue="TRUE" falsevalue="FALSE" /> <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' /> <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.' /> <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.' /> <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).' /> <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' /> <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/> </inputs> <outputs> <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells-tsne.rds" ftype="rdata" /> <output name="output_image_file" > <assert_contents> <has_size value="18122" delta="4000"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Graphs the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique. By default, cells are colored by their identity class (can be changed with the group.by parameter). @SEURAT_INTRO@ ----- **Inputs** * Seurat RDS object ----- **Outputs** * PNG-format image file .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>