comparison seurat_scale_data.xml @ 0:6166efaeb4a6 draft

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 11:18:45 -0400
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children 3d0bfc2a233e
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1 <tool id="seurat_scale_data" name="Seurat ScaleData" version="2.3.1+galaxy1">
2 <description>scale and center 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-scale-data.R
10
11 --input-object-file '$input'
12 #if $vars:
13 --vars-to-regress '$vars'
14 #else
15 --vars-to-regress nUMI
16 #end if
17
18 #if $genes:
19 --genes-use '$genes'
20 #end if
21
22 --model-use '$model'
23
24 $use_umi
25 $do_center
26
27 #if $scale_max:
28 --scale-max '$scale_max'
29 #end if
30
31 #if $block_size:
32 --block-size '$block_size'
33 #end if
34
35 #if $min_cells_to_block:
36 --min-cells-to-block '$min_cells_to_block'
37 #end if
38
39 $check_for_norm
40
41
42
43 --output-object-file '$output'
44 ]]></command>
45
46 <inputs>
47 <param name="input" argument="--input-object-file" type='data' format='rdata' help="File name in where a serialized R matrix object can be found." label="Seurat RDS object"/>
48 <param name="genes" argument="--genes-use" type='data' format='txt' optional='true' help="File to be used to derive a vector of gene names to scale/center (one gene per line). Default is all genes in object@data."/>
49 <param name="vars" argument="--vars-to-regress" type='text' optional='True' label="Vars to regress" help="Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito."/>
50 <param name="model" argument="--model-use" type="select" label="Statistical model" help="Use a linear model or generalized linear model (poisson, negative binomial) for the regression.">
51 <option value="linear" selected="true">Linear model</option>
52 <option value="poisson">Poisson model</option>
53 <option value="negbinom">Negative binomial model</option>
54 </param>
55 <param name="use_umi" argument="--use-umi" type="boolean" truevalue="--use-umi TRUE" falsevalue="" checked="false" label="Use UMIs." help="Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'."/>
56 <param name="do_center" argument="--do-center" type="boolean" falsevalue="--do-center FALSE" truevalue="" checked="true" label="Perform centering" help="Whether to center the data."/>
57 <param name="scale_max" argument="--scale-max" optional="true" type="float" label="Scale maximum" help = "Max value to return for scaled data. The default is 10. Setting this can help reduce the effects of genes that are only expressed in a very small number of cells. If regressing out latent variables and using a non-linear model, the default is 50."/>
58 <param name="block_size" argument="--block-size" optional="true" type="integer" label="Block size" help = "Default size for number of genes to scale at in a single computation. Increasing block.size may speed up calculations but at an additional memory cost. Defaults to 1000 if not specified."/>
59 <param name="min_cells_to_block" argument="--min-cells-to-block" optional="true" type="integer" label="Minimum number of cells to block" help="If object contains fewer than this number of cells, don't block for scaling calculations. Defaults to 1000."/>
60 <param name="check_for_norm" argument="--check-for-norm" optional="true" type="boolean" falsevalue="--check-for-norm FALSE" truevalue="" label="Check that data is normalized" help="Check to see if data has been normalized, if not, output a warning (TRUE by default). Data can be normalised by Seurat normalise module."/>
61 </inputs>
62
63 <outputs>
64 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
65 </outputs>
66
67 <tests>
68 <test>
69 <param name="input" ftype="rdata" value="out_findvar.rds"/>
70 <output name="output" ftype="rdata" value="out_scale.rds" compare="sim_size"/>
71 </test>
72 </tests>
73 <help><![CDATA[
74 .. class:: infomark
75
76 **What it does**
77
78 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
79 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
80 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
81 types of single cell data.
82
83 This tool regresses out variables in a Seurat object to mitigate the effect of confounding factors.
84
85
86 -----
87
88 **Inputs**
89
90 * Seurat RDS object, probably normalised.
91 * Genes to use. A file with a vector of gene names to scale/center (one gene per line). Default is all genes in object@data.
92 * Variables to regress
93 * Statistical model to use.
94 * Use UMIs (boolean)
95 * Do centering (boolean)
96 * Scale maximum
97 * Block size
98 * Minimum number of cells to block
99 * Check that data is normalised
100
101 -----
102
103 **Outputs**
104
105 * Seurat RDS object, scaled.
106
107 .. _Seurat: https://www.nature.com/articles/nbt.4096
108 .. _Satija Lab: https://satijalab.org/seurat/
109
110 @VERSION_HISTORY@
111 ]]></help>
112 <expand macro="citations" />
113 </tool>