Mercurial > repos > ebi-gxa > seurat_normalise_data

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planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
author ebi-gxa
date Sun, 01 Oct 2023 09:07:32 +0000
parents ce141a4e433e
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1 <tool id="seurat_normalise_data" name="Seurat NormaliseData" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
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2 <description>normalise data</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-normalise-data.R
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10
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11 @INPUT_OBJECT@
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12 #if $norm:
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13 --normalization-method $norm
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14 #end if
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15 #if $assay:
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16 --assay-type '$assay'
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17 #end if
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18 #if $scale:
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19 --scale-factor $scale
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20 #end if
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21 @OUTPUT_OBJECT@
0
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22 ]]></command>
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24 <inputs>
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25 <expand macro="input_object_params"/>
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26 <expand macro="output_object_params"/>
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27 <param name="norm" argument="--normalization-method" type="select" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize). Can be 'CLR' or 'RC' additionally.">
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28 <option value="LogNormalize" selected="true">Log Normalise</option>
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29 <option value="CLR">CLR</option>
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30 <option value="RC">RC</option>
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31 </param>
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32 <param name="assay" argument="--assay-type" type="text" optional="True" label="Assay type" help = "Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses.">
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33 <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator>
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34 </param>
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35 <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/>
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36 </inputs>
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37
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38 <outputs>
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39 <expand macro="output_files"/>
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40 </outputs>
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42 <tests>
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43 <test>
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44 <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells.rds"/>
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45 <output name="rds_seurat_file" ftype="rdata">
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46 <assert_contents>
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47 <has_size value="2720178" delta="200000"/>
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48 </assert_contents>
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49 </output>
0
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 .. class:: infomark
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54
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55 **What it does**
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56
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57 This tool normalises a Seurat RDS object.
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58
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59 @SEURAT_INTRO@
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61 -----
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63 **Inputs**
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64
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65 * Seurat RDS object. Possibly the output of Seurat filter cells or Seurat create object.
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66 * Normalisation method. Method for normalization. Default is log-normalization (LogNormalize).
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67 * Assay type. Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses.
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68 * Scale factor. Sets the scale factor for cell-level normalization. Default: 1000
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70 -----
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72 **Outputs**
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73
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74 * Seurat RDS object with normalised matrix.
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75
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76 .. _Seurat: https://www.nature.com/articles/nbt.4096
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77 .. _Satija Lab: https://satijalab.org/seurat/
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78
1
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79 @VERSION_HISTORY@
0
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80 ]]></help>
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81 <expand macro="citations" />
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82 </tool>