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author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:20:42 -0400 |
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children | 48174ec556de |
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<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="2.3.1+galaxy1"> <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-file '$input' #if $norm: --normalization-method $norm #end if #if $assay: --assay-type '$assay' #end if #if $scale: --scale-factor $scale #end if --output-object-file '$output' ]]></command> <inputs> <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Possibly the output of Seurat filter cells or Seurat create object." /> <param name="norm" argument="--normalization-method" type="text" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize)."/> <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">^[\(\w\)]+$</validator> </param> <param name="scale" argument="--scale-factor" type="integer" optional="True" label="Scale factor" help="Sets the scale factor for cell-level normalization"/> </inputs> <outputs> <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/> </outputs> <tests> <test> <param name="input" ftype="rdata" value="seurat.rds"/> <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. This tool normalises a Seurat RDS object. ----- **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>