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author | ebi-gxa |
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date | Sat, 02 Mar 2024 10:42:30 +0000 |
parents | a835b38e389f |
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<tool id="seurat_normalise_data" name="Seurat NormaliseData" profile="18.01" version="@SEURAT_VERSION@+galaxy0"> <description>normalise data</description> <macros> <import>seurat_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version" /> <command detect_errors="exit_code"><![CDATA[ seurat-normalise-data.R @INPUT_OBJECT@ #if $norm: --normalization-method $norm #end if #if $assay: --assay-type '$assay' #end if #if $scale: --scale-factor $scale #end if @OUTPUT_OBJECT@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <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."> <option value="LogNormalize" selected="true">Log Normalise</option> <option value="CLR">CLR</option> <option value="RC">RC</option> </param> <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."> <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator> </param> <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> </inputs> <outputs> <expand macro="output_files"/> </outputs> <tests> <test> <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells.rds"/> <output name="rds_seurat_file" ftype="rdata"> <assert_contents> <has_size value="2720178" delta="200000"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool normalises a Seurat RDS object. @SEURAT_INTRO@ ----- **Inputs** * Seurat RDS object. Possibly the output of Seurat filter cells or Seurat create object. * Normalisation method. Method for normalization. Default is log-normalization (LogNormalize). * Assay type. Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses. * Scale factor. Sets the scale factor for cell-level normalization. Default: 1000 ----- **Outputs** * Seurat RDS object with normalised matrix. .. _Seurat: https://www.nature.com/articles/nbt.4096 .. _Satija Lab: https://satijalab.org/seurat/ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>