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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 11:17:53 -0400
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1 <tool id="seurat_find_variable_genes" name="Seurat FindVariableGenes" version="2.3.1+galaxy1">
2 <description>identify variable genes</description>
3 <macros>
4 <import>seurat_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[
9 seurat-find-variable-genes.R
10
11 --input-object-file '$input'
12 #if $mean:
13 --mean-function '$mean'
14 #end if
15 #if $disp:
16 --dispersion-function $disp
17 #end if
18 #if $xlow:
19 --x-low-cutoff $xlow
20 #end if
21 #if $xhigh:
22 --x-high-cutoff $xhigh
23 #end if
24 #if $ylow:
25 --y-low-cutoff $ylow
26 #end if
27 #if $yhigh:
28 --y-high-cutoff $yhigh
29 #end if
30 --output-object-file '$output'
31 --output-text-file '$output_tab'
32 ]]></command>
33
34 <inputs>
35 <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="R serialized object for Seurat, normally the one produced by Seurat FindVariableGenes" />
36 <param name="mean" argument="--mean-function" type="text" optional="True" label="Mean function" help="Function to compute x-axis value (average expression). Default is to take the mean of the detected (i.e. non-zero) values."/>
37 <param name="disp" argument="--dispersion-function" type="text" optional="True" label="Dispersion function" help="Function to compute y-axis value (dispersion). Default is to take the standard deviation of all values." />
38 <param name="xlow" argument="--x-low-cutoff" type="float" optional="True" label="X-axis low cutoff" help="Bottom cutoff on x-axis for identifying variable genes."/>
39 <param name="xhigh" argument="--x-high-cutoff" type="float" optional="True" label="X-axis high cutoff" help="Top cutoff on x-axis for identifying variable genes."/>
40 <param name="ylow" argument="--y-low-cutoff" type="float" optional="True" label="Y-axis low cutoff" help="Bottom cutoff on y-axis for identifying variable genes."/>
41 <param name="yhigh" argument="--y-high-cutoff" type="float" optional="True" label="Y-axis high cutoff" help="Top cutoff on y-axis for identifying variable genes."/>
42 </inputs>
43
44 <outputs>
45 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
46 <data name="output_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Variable genes tabular file"/>
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="input" ftype="rdata" value="out_norm.rds"/>
52 <output name="output" ftype="rdata" value="out_findvar.rds" compare="sim_size"/>
53 </test>
54 </tests>
55 <help><![CDATA[
56 .. class:: infomark
57
58 **What it does**
59
60 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
61 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
62 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
63 types of single cell data.
64
65 This tool identifies genes that are outliers on a 'mean variability plot'. First, uses
66 a function to calculate average expression (mean.function) and dispersion (dispersion.function)
67 for each gene. Next, divides genes into num.bin (deafult 20) bins based on
68 their average expression, and calculates z-scores for dispersion within each
69 bin. The purpose of this is to identify variable genes while controlling for
70 the strong relationship between variability and average expression.
71
72 Exact parameter settings may vary empirically from dataset to dataset, and
73 based on visual inspection of the plot.
74
75 Setting the y.cutoff parameter to 2 identifies genes that are more than two standard
76 deviations away from the average dispersion within a bin. The default X-axis function
77 is the mean expression level, and for Y-axis it is the log(Variance/mean). All mean/variance
78 calculations are not performed in log-space, but the results are reported in log-space -
79 see relevant functions for exact details.
80
81 -----
82
83 **Inputs**
84
85 * Seurat RDS object
86 * Mean function. Function to compute x-axis value (average expression). Default is to take the mean of the detected (i.e. non-zero) values.
87 * Dispersion function. Function to compute y-axis value (dispersion). Default is to take the standard deviation of all values.
88 * Bottom cutoff on x-axis for identifying variable genes.
89 * Top cutoff on x-axis for identifying variable genes.
90 * Bottom cutoff on y-axis for identifying variable genes.
91 * Top cutoff on y-axis for identifying variable genes.
92
93 -----
94
95 **Outputs**
96
97 * Seurat RDS object. Places variable genes in object@var.genes. The result of all analysis is stored in object@hvg.info
98 * Tabular file of variable genes
99
100 .. _Seurat: https://www.nature.com/articles/nbt.4096
101 .. _Satija Lab: https://satijalab.org/seurat/
102
103 @VERSION_HISTORY@
104 ]]></help>
105 <expand macro="citations" />
106 </tool>