annotate seurat_run_pca.xml @ 1:c4607a42113e draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author ebi-gxa
date Mon, 25 Nov 2019 06:08:09 -0500
parents df80f3d2f9d4
children e534a73143b1
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1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
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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@
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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 #if $pc_cells
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16 --pc-cells '$pc_cells'
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17 #end if
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18 @OUTPUT_OBJECT@
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19 --output-embeddings-file output_embed
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20 --output-loadings-file output_load
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21 --output-stdev-file output_sdev
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22 #if $pcs_compute:
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23 --pcs-compute '$pcs_compute'
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24 #end if
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25 #if $reverse_pca
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26 '$reverse_pca'
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27 #end if
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28
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29 ]]></command>
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31 <inputs>
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32 <expand macro="input_object_params"/>
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33 <expand macro="output_object_params"/>
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34 <param name="pc_genes" type="data" format="tabular,txt" optional="True" label="Genes to scale" help="File with gene names to scale/center. Default is all genes in object@data." />
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35 <param label="Cells to scale" optional="true" name="pc_cells" argument="--pc-cells" type="text" help="File with cell names to scale/center. Default is all cells in object@data."/>
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36 <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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37 <param label="Reverse PCA" optional="true" name="reverse_pca" argument="--reverse-pca" type="boolean" truevalue="--reverse-pca" checked="false" help="Run PCA on reverse matrix (gene x cell; FALSE by default means cell x gene)."/>
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38 </inputs>
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39
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40 <outputs>
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41 <expand macro="output_files"/>
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42 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
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43 <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
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44 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="input" ftype="rdata" value="out_scale.rds"/>
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50 <output name="rds_seurat_file" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 .. class:: infomark
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55
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56 **What it does**
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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 @SEURAT_INTRO@
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61
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62 -----
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63
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64 **Inputs**
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65
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66 * Seurat RDS object, normalised and scaled potentially.
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67 * Genes used to scale. File of gene names to scale/center. Default is all genes in object.
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68 * 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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69 * Use imputed. Boolean indicating whether to run PCA on imputed values or not.
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70
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71 -----
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72
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73 **Outputs**
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74
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75 * Seurat RDS object with PCA calculations and embeddings.
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76 * Embeddings on CSV file. File with a csv-format embeddings table with principal components by cell.
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77 * Loadings on CSV file. File with a csv-format loadings table with principal components by gene.
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78 * Standard deviation on CSV file. Contains principal components std. deviations.
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79
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80 .. _Seurat: https://www.nature.com/articles/nbt.4096
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81 .. _Satija Lab: https://satijalab.org/seurat/
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82
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83 @VERSION_HISTORY@
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84 ]]></help>
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85 <expand macro="citations" />
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86 </tool>