Mercurial > repos > ebi-gxa > seurat_run_pca

annotate seurat_run_pca.xml @ 0:df80f3d2f9d4 draft

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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 11:15:42 -0400
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df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="2.3.1+galaxy1">
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2 <description>run a PCA 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-pca.R
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10
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11 --input-object-file '$input'
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12 #if $pc_genes:
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13 --pc-genes '$pc-genes'
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14 #end if
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15 --output-object-file '$output'
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16 --output-embeddings-file output_embed
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17 --output-loadings-file output_load
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18 --output-stdev-file output_sdev
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19 #if $pcs_compute:
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20 --pcs-compute '$pcs_compute'
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21 #end if
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22 #if $use_imputed:
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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23 '$use_imputed'
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24 #end if
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25
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="input" type="data" format="rdata" label="RDS object" />
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30 <param name="pc_genes" type="data" format="tabular, txt" optional="True" label="Genes to scale" help="File of gene names to scale/center. Default is all genes in object." />
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31 <param name="pcs_compute" type="integer" optional="True" label="Principal components" help="Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance."/>
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32 <param name="use_imputed" type="boolean" truevalue="--use-imputed TRUE" falsevalue="" checked="false" label="Use imputed" help="Run PCA on imputed values."/>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
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37 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
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38 <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
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39 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <param name="input" ftype="rdata" value="out_scale.rds"/>
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45 <output name="output" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 .. class:: infomark
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50
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51 **What it does**
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52
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53 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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54 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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55 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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56 types of single cell data.
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57
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58 This tool runs a PCA dimensionality reduction
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59
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60 -----
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61
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62 **Inputs**
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63
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64 * Seurat RDS object, normalised and scaled potentially.
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65 * Genes used to scale. File of gene names to scale/center. Default is all genes in object.
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66 * Principal components to compute. Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance.
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67 * Use imputed. Boolean indicating whether to run PCA on imputed values or not.
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68
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69 -----
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70
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71 **Outputs**
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73 * Seurat RDS object with PCA calculations and embeddings.
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74 * Embeddings on CSV file. File with a csv-format embeddings table with principal components by cell.
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75 * Loadings on CSV file. File with a csv-format loadings table with principal components by gene.
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76 * Standard deviation on CSV file. Contains principal components std. deviations.
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77
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78 .. _Seurat: https://www.nature.com/articles/nbt.4096
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79 .. _Satija Lab: https://satijalab.org/seurat/
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80
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81 @VERSION_HISTORY@
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82 ]]></help>
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83 <expand macro="citations" />
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84 </tool>