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planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
author ebi-gxa
date Sun, 01 Oct 2023 09:07:05 +0000
parents 52ccdd3fb5e8
children
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1 <tool id="seurat_scale_data" name="Seurat ScaleData" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
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2 <description>scale and center genes</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 seurat-scale-data.R
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11 @INPUT_OBJECT@
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12 #if $vars:
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13 --vars-to-regress '$vars'
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14 #else
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15 --vars-to-regress nUMI
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16 #end if
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18 #if $genes_use:
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19 --genes-use '$genes_use'
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20 #end if
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22 --model-use '$model'
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24 $use_umi
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25 $do_not_center
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27 #if $scale_max:
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28 --scale-max '$scale_max'
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29 #end if
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31 #if $block_size:
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32 --block-size '$block_size'
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33 #end if
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35 #if $min_cells_to_block:
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36 --min-cells-to-block '$min_cells_to_block'
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37 #end if
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39 $check_for_norm
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40
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41 @OUTPUT_OBJECT@
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42 ]]></command>
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44 <inputs>
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45 <expand macro="input_object_params"/>
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46 <expand macro="output_object_params"/>
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47 <expand macro="genes-use-input"/>
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48 <param name="vars" argument="--vars-to-regress" type='text' value="nCount_RNA" label="Vars to regress" help="Comma-separated list of variables to regress out (previously latent.vars in RegressOut). For example, nCount_RNA, or percent.mito.">
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49 <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator>
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50 <option value="nCount_RNA">nCount_RNA</option>
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51 <option value="nFeature_RNA">nFeature_RNA</option>
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52 </param>
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53 <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.">
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54 <option value="linear" selected="true">Linear model</option>
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55 <option value="poisson">Poisson model</option>
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56 <option value="negbinom">Negative binomial model</option>
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57 </param>
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58 <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'."/>
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59 <param name="do_not_center" argument="--do-not-center" type="boolean" falsevalue="" truevalue="--do-not-center" checked="false" label="Skip centering" help="By default data is centered, with this option you can skip centering."/>
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60 <param name="do_not_scale" argument="--do-not-scale" type="boolean" falsevalue="" truevalue="--do-not-scale" checked="false" label="Skip scaling" help="By default data is scaled, with this option you can skip scaling."/>
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61 <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."/>
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62 <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."/>
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63 <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."/>
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64 <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."/>
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65 </inputs>
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66
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67 <outputs>
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68 <expand macro="output_files"/>
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69 </outputs>
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71 <tests>
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72 <test>
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73 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-fvg.rds"/>
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74 <param name="vars_to_regress" value="nCount_RNA" />
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75 <param name="use_umi" value="True" />
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76 <output name="rds_seurat_file" ftype="rdata">
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77 <assert_contents>
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78 <has_size value="4233990" delta="200000"/>
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79 </assert_contents>
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80 </output>
0
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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 This tool regresses out variables in a Seurat object to mitigate the effect of confounding factors.
2890cec5229f planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit fc12e1e90bdc675bd81cf50528afd64ff3dc5c08
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89
2
52ccdd3fb5e8 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
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90 @SEURAT_INTRO@
0
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91
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92 -----
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93
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94 **Inputs**
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95
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96 * Seurat RDS object, probably normalised.
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97 * 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.
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98 * Variables to regress
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99 * Statistical model to use.
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100 * Use UMIs (boolean)
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101 * Do centering (boolean)
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102 * Scale maximum
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103 * Block size
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104 * Minimum number of cells to block
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105 * Check that data is normalised
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106
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107 -----
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108
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109 **Outputs**
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110
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111 * Seurat RDS object, scaled.
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112
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113 .. _Seurat: https://www.nature.com/articles/nbt.4096
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114 .. _Satija Lab: https://satijalab.org/seurat/
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115
1
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116 @VERSION_HISTORY@
0
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117 ]]></help>
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118 <expand macro="citations" />
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119 </tool>