Mercurial > repos > ebi-gxa > seurat_find_variable_genes

annotate seurat_find_variable_genes.xml @ 5:5be60722113a draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:26:36 +0000
parents 051953328516
children
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5be60722113a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
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1 <tool id="seurat_find_variable_genes" name="Seurat FindVariableGenes" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
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2 <description>identify variable 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-find-variable-genes.R
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10
1
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11 @INPUT_OBJECT@
0
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12 #if $mean:
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13 --mean-function '$mean'
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14 #end if
1
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15 #if $selection_method
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16 --selection-method '$selection_method'
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17 #end if
0
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18 #if $disp:
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19 --dispersion-function $disp
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20 #end if
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21 #if $xlow:
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22 --x-low-cutoff $xlow
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23 #end if
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24 #if $xhigh:
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25 --x-high-cutoff $xhigh
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26 #end if
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27 #if $ylow:
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28 --y-low-cutoff $ylow
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29 #end if
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30 #if $yhigh:
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31 --y-high-cutoff $yhigh
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32 #end if
1
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33 @OUTPUT_OBJECT@
0
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34 --output-text-file '$output_tab'
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35 ]]></command>
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36
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37 <inputs>
1
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38 <expand macro="input_object_params"/>
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39 <expand macro="output_object_params"/>
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40 <param label="Number of features" optional="true" name="nfeatures" argument="--nfeatures" type="integer" help="Number of features to return."/>
0
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41 <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."/>
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42 <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." />
1
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43 <param name="xlow" argument="--x-low-cutoff" type="float" optional="True" label="X-axis low cutoff" help="Bottom cutoff on x-axis (mean) for identifying variable genes."/>
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44 <param name="xhigh" argument="--x-high-cutoff" type="float" optional="True" label="X-axis high cutoff" help="Top cutoff on x-axis (mean) for identifying variable genes."/>
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45 <param name="ylow" argument="--y-low-cutoff" type="float" optional="True" label="Y-axis low cutoff" help="Bottom cutoff on y-axis (dispersion) for identifying variable genes."/>
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46 <param name="yhigh" argument="--y-high-cutoff" type="float" optional="True" label="Y-axis high cutoff" help="Top cutoff on y-axis (dispersion) for identifying variable genes."/>
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47 <param label="Selection method" optional="true" name="selection_method" argument="--selection-method" type="select" help="How to choose top variable features. Choose one of: 'vst', 'mvp', disp.">
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48 <option value="vst" selected="true">vst</option>
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49 <option value="mbp">mbp</option>
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50 <option value="disp">disp</option>
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51 </param>
0
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52 </inputs>
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53
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54 <outputs>
1
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55 <expand macro="output_files"/>
0
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56 <data name="output_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Variable genes tabular file"/>
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57 </outputs>
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58
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59 <tests>
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60 <test>
5
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61 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-normalised.rds"/>
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62 <output name="rds_seurat_file" ftype="rdata">
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63 <assert_contents>
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64 <has_size value="2720178" delta="200000"/>
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65 </assert_contents>
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66 </output>
0
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 .. class:: infomark
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71
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72 **What it does**
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73
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74 This tool identifies genes that are outliers on a 'mean variability plot'. First, uses
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75 a function to calculate average expression (mean.function) and dispersion (dispersion.function)
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76 for each gene. Next, divides genes into num.bin (deafult 20) bins based on
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77 their average expression, and calculates z-scores for dispersion within each
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78 bin. The purpose of this is to identify variable genes while controlling for
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79 the strong relationship between variability and average expression.
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80
1
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81 For the mean.var.plot method: Exact parameter settings may vary empirically from
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82 dataset to dataset, and based on visual inspection of the plot. Setting the
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83 y.cutoff parameter to 2 identifies features that are more than two standard deviations
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84 away from the average dispersion within a bin. The default X-axis function is the
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85 mean expression level, and for Y-axis it is the log(Variance/mean). All
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86 mean/variance calculations are not performed in log-space, but the results are
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87 reported in log-space - see relevant functions for exact details.
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88
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89 @SEURAT_INTRO@
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90
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91 -----
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92
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93 **Inputs**
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94
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95 * Seurat RDS object
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96 * Mean function. Function to compute x-axis value (average expression). Default is to take the mean of the detected (i.e. non-zero) values.
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97 * Dispersion function. Function to compute y-axis value (dispersion). Default is to take the standard deviation of all values.
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98 * Bottom cutoff on x-axis for identifying variable genes.
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99 * Top cutoff on x-axis for identifying variable genes.
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100 * Bottom cutoff on y-axis for identifying variable genes.
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101 * Top cutoff on y-axis for identifying variable genes.
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102
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103 -----
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104
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105 **Outputs**
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106
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107 * Seurat RDS object. Places variable genes in object@var.genes. The result of all analysis is stored in object@hvg.info
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108 * Tabular file of variable genes
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109
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110 .. _Seurat: https://www.nature.com/articles/nbt.4096
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111 .. _Satija Lab: https://satijalab.org/seurat/
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112
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113 @VERSION_HISTORY@
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114 ]]></help>
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115 <expand macro="citations" />
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116 </tool>