<tool id="seurat_normalise_data" name="Seurat NormaliseData" 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="filtered_seurat.rds"/>
            <output name="rds_seurat_file" ftype="rdata" value="normalised_seurat.rds" compare="sim_size" delta="1000000"/>
        </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>