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comparison seurat_dim_plot.xml @ 1:daeca8f7a26e draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author ebi-gxa
date Mon, 25 Nov 2019 06:12:13 -0500
parents 6e26ee99fdfc
children 34f8d81f9d75
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0:6e26ee99fdfc 1:daeca8f7a26e
1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0"> 1 <tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="@SEURAT_VERSION@_@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" />
7 <expand macro="version" /> 7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 seurat-dim-plot.R 9 seurat-dim-plot.R
10 --input-object-file '$input' 10 @INPUT_OBJECT@
11 #if $reduction_use 11 #if $reduction_use
12 --reduction-use '$reduction_use' 12 --reduction-use '$reduction_use'
13 #end if 13 #end if
14 #if $dim_1 14 #if $dim_1
15 --dim-1 $dim_1 15 --dim-1 $dim_1
49 --png-width $png_width 49 --png-width $png_width
50 --png-height $png_height 50 --png-height $png_height
51 --output-image-file $output_image_file 51 --output-image-file $output_image_file
52 ]]></command> 52 ]]></command>
53 <inputs> 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'/> 54 <expand macro="input_object_params"/>
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' /> 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' /> 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' /> 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'/> 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' /> 59 <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
83 <help><![CDATA[ 83 <help><![CDATA[
84 .. class:: infomark 84 .. class:: infomark
85 85
86 **What it does** 86 **What it does**
87 87
88 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing 88 Graphs the output of a dimensional reduction technique on a 2D scatter plot
89 data. It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to 89 where each point is a cell and it's positioned based on the cell embeddings
90 identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to 90 determined by the reduction technique. By default, cells are colored by their
91 integrate diverse types of single cell data. 91 identity class (can be changed with the group.by parameter).
92 92
93 This tool graphs the output of a dimensional reduction technique (PCA by default). Cells are colored 93 @SEURAT_INTRO@
94 by their identity class.
95 94
96 ----- 95 -----
97 96
98 **Inputs** 97 **Inputs**
99 98