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<tool id="seurat_run_tsne" name="Seurat RunTSNE" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
    <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@
#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
#if $adv.tsne_method
  --tsne-method '$adv.tsne_method'
#end if
#if $adv.dim_embed
  --dim_embed '$adv.dim_embed'
#end if
#if $adv.random_seed
  --random-seed '$adv.random_seed'
#end if
#if $adv.perplexity
  --perplexity '$adv.perplexity'
#end if

@OUTPUT_OBJECT@
--output-embeddings-file output_embed
]]></command>

    <inputs>
        <expand macro="input_object_params"/>
        <expand macro="output_object_params"/>
        <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."/>
            <param label="tSNE method" optional="true" name="tsne_method" argument="--tsne-method" type="select" help="Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE">
              <option value="Rtsne" selected="true">Rtsne</option>
              <option value="Flt-SNE">Flt-SNE</option>
            </param>
            <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE">
              <option value="2" selected="true">2</option>
              <option value="3">3</option>
            </param>
            <param label="Perplexity" optional="true" name="perplexity" argument="--perplexity" type="integer" help="An integer above 0."/>
            <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/>
        </section>
    </inputs>

    <outputs>
        <expand macro="output_files"/>
        <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
    </outputs>

    <tests>
        <test>
            <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-clusters.rds"/>
            <output name="rds_seurat_file" ftype="rdata" >
              <assert_contents>
                <has_size value="5067150" delta="200000"/>
              </assert_contents>
            </output>
        </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.

-----

**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>