Mercurial > repos > ebi-gxa > seurat_run_pca

annotate seurat_run_pca.xml @ 6:8ded486b0014 draft default tip

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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:48 +0000
parents 9547ebb03f6f
children
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1 <tool id="seurat_run_pca" name="Seurat RunPCA" profile="18.01" version="@SEURAT_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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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>
1
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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>
5
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49 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-scaled.rds"/>
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50 <output name="rds_seurat_file" ftype="rdata">
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51 <assert_contents>
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52 <has_size value="5052296" delta="200000"/>
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53 </assert_contents>
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54 </output>
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55 <output name="output_embed" >
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56 <assert_contents>
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57 <has_n_lines n="92"/>
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58 </assert_contents>
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59 </output>
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60 <output name="output_load" >
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61 <assert_contents>
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62 <has_n_lines n="2001"/>
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63 </assert_contents>
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64 </output>
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65 <output name="output_sdev" >
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66 <assert_contents>
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67 <has_n_lines n="50"/>
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68 </assert_contents>
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69 </output>
0
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 .. class:: infomark
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74
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75 **What it does**
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76
1
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77 This tool runs a PCA dimensionality reduction.
0
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78
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79 @SEURAT_INTRO@
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80
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81 -----
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82
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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83 **Inputs**
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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84
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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85 * Seurat RDS object, normalised and scaled potentially.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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86 * Genes used to scale. File of gene names to scale/center. Default is all genes in object.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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87 * 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.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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88 * Use imputed. Boolean indicating whether to run PCA on imputed values or not.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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89
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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90 -----
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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91
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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92 **Outputs**
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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93
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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94 * Seurat RDS object with PCA calculations and embeddings.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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95 * Embeddings on CSV file. File with a csv-format embeddings table with principal components by cell.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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96 * Loadings on CSV file. File with a csv-format loadings table with principal components by gene.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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97 * Standard deviation on CSV file. Contains principal components std. deviations.
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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98
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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99 .. _Seurat: https://www.nature.com/articles/nbt.4096
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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100 .. _Satija Lab: https://satijalab.org/seurat/
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101
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102 @VERSION_HISTORY@
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103 ]]></help>
df80f3d2f9d4 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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104 <expand macro="citations" />
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105 </tool>