annotate seurat_create_object.xml @ 0:f8865ae30723 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<tool id="seurat_create_seurat_object" name="Seurat CreateSeuratObject" version="2.3.1+galaxy0">
    <description>create a Seurat object</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
seurat-create-seurat-object.R

--input-object-file '$input'
--output-object-file '$output'
]]></command>

    <inputs>
        <param name="input" type="data" format="rdata" label="Seurat object" help="RDS file from Seurat read10x module." />
    </inputs>

    <outputs>
        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="rdata" value="deng.rds"/>
            <output name="output" ftype="rdata" value="seurat.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 creates a Seurat object from an RDS object.

-----

**Inputs**

    * RDS object from Seurat read_10x module.

-----

**Outputs**

    * Seurat RDS object

.. _Seurat: https://www.nature.com/articles/nbt.4096
.. _Satija Lab: https://satijalab.org/seurat/

@VERSION_HISTORY@

]]></help>
      <expand macro="citations" />
</tool>