comparison seurat_normalise_data.xml @ 1:48174ec556de draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f

0:619fead82856

<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**

1:48174ec556de

<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="@SEURAT_VERSION@_@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="input" ftype="rdata" value="seurat.rds"/>
            <output name="rds_seurat_file" ftype="rdata" value="out_norm.rds" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool normalises a Seurat RDS object.

@SEURAT_INTRO@

-----

**Inputs**