Mercurial > repos > ebi-gxa > seurat_run_tsne

annotate seurat_run_tsne.xml @ 5:8d9ceaec2c7f 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 07:27:38 +0000
parents 2d294978b152
children
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8d9ceaec2c7f "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_run_tsne" name="Seurat RunTSNE" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
0
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2 <description>run t-SNE dimensionality reduction</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-run-tsne.R
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10
1
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11 @INPUT_OBJECT@
0
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12 #if $genes_use:
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13 --genes-use '$genes_use'
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14 #end if
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16 #if str($adv.dims_use):
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17 --dims-use \$(seq -s , 1 '$adv.dims_use')
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18 #else
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19 --dims-use 1,10
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20 #end if
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21
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22 #if not $adv.do_fast:
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23 --do-fast '$adv.do_fast'
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24 #end if
1
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25 #if $adv.tsne_method
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26 --tsne-method '$adv.tsne_method'
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27 #end if
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28 #if $adv.dim_embed
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29 --dim_embed '$adv.dim_embed'
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30 #end if
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31 #if $adv.random_seed
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32 --random-seed '$adv.random_seed'
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33 #end if
2
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34 #if $adv.perplexity
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35 --perplexity '$adv.perplexity'
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36 #end if
0
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37
1
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38 @OUTPUT_OBJECT@
0
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39 --output-embeddings-file output_embed
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40 ]]></command>
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41
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42 <inputs>
1
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43 <expand macro="input_object_params"/>
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44 <expand macro="output_object_params"/>
0
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45 <expand macro="genes-use-input"/>
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46 <section name="adv" title="Advanced Options">
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47 <expand macro="dims-use-input"/>
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48 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/>
1
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49 <param label="tSNE method" optional="true" name="tsne_method" argument="--tsne-method" type="select" help="Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE">
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50 <option value="Rtsne" selected="true">Rtsne</option>
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51 <option value="Flt-SNE">Flt-SNE</option>
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52 </param>
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53 <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE">
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54 <option value="2" selected="true">2</option>
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55 <option value="3">3</option>
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56 </param>
2
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57 <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/>
1
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58 <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
0
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59 </section>
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60 </inputs>
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61
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62 <outputs>
1
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63 <expand macro="output_files"/>
0
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64 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
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65 </outputs>
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66
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67 <tests>
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68 <test>
5
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69 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-clusters.rds"/>
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70 <output name="rds_seurat_file" ftype="rdata" >
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71 <assert_contents>
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72 <has_size value="5067150" delta="200000"/>
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73 </assert_contents>
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74 </output>
0
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 .. class:: infomark
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79
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80 **What it does**
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81
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82 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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83 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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84 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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85 types of single cell data.
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86
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87 Run t-SNE dimensionality reduction on selected features. Has the option of running
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88 in a reduced dimensional space (i.e. spectral tSNE, recommended), or
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89 running based on a set of genes.
0
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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 * RDS object
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96
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97 -----
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98
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99 **Outputs**
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100
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101 * Seurat RDS object
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102
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103 .. _Seurat: https://www.nature.com/articles/nbt.4096
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104 .. _Satija Lab: https://satijalab.org/seurat/
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105
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106 @VERSION_HISTORY@
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107 ]]></help>
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108 <expand macro="citations" />
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109 </tool>