<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1">
    <description>run t-SNE dimensionality reduction</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
seurat-run-tsne.R

--input-object-file '$input'

#if $genes_use:
  --genes-use '$genes_use'
#end if

#if str($adv.dims_use):
    --dims-use \$(seq -s , 1 '$adv.dims_use')
#else
    --dims-use 1,10
#end if

#if not $adv.do_fast:
    --do-fast '$adv.do_fast'
#end if

--output-object-file '$output'
--output-embeddings-file output_embed
]]></command>

    <inputs>
        <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/>
        <expand macro="genes-use-input"/>
        <section name="adv" title="Advanced Options">
            <expand macro="dims-use-input"/>
            <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/>
        </section>
    </inputs>

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

    <tests>
        <test>
            <param name="input" ftype="rdata" value="out_findclust.rds"/>
            <output name="output" ftype="rdata" value="out_runtsne.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.

Run t-SNE dimensionality reduction on selected features. Has the option of
running in a reduced dimensional space (i.e. spectral tSNE, recommended),
or running based on a set of genes. For details about stored TSNE calculation
parameters, see standard output of the tool.

-----

**Inputs**

    * RDS object

-----

**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>