<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="2.3.1+galaxy0">
    <description>graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
        seurat-dim-plot.R
        --input-object-file '$input'
        #if $reduction_use
        --reduction-use '$reduction_use'
        #end if
        #if $dim_1
        --dim-1 $dim_1
        #end if
        #if $dim_2
        --dim-2 $dim_2
        #end if
        #if $cells_use
        --cells-use $cells_use
        #end if
        #if $pt_size
        --pt-size $pt_size
        #end if
        #if $label_size
        --label-size $label_size
        #end if
        --do-label $do_label
        #if $group_by
        --group-by $group_by
        #end if
        #if $plot_title
        --plot-title '$plot_title'
        #end if
        --do-bare $do_bare
        #if $cols_use
        --cols-use '$cols_use'
        #end if
        #if $pt_shape
        --pt-shape '$pt_shape'
        #end if
        --coord-fixed $coord_fixed
        --no-axes $no_axes
        --dark-theme $dark_theme
        #if $plot_order
        --plot-order '$plot_order'
        #end if
        --png-width $png_width
        --png-height $png_height
        --output-image-file $output_image_file
    ]]></command>
    <inputs>
        <param type="data" name="input" format="rdata" label="RDS object" help='File in which a serialized R matrix object may be found'/>
        <param type="text" name="reduction_use" value='pca' label="Dimensionality reduction" help='Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed' />
        <param type="integer" name="dim_1" value='1' label="X axis dimension" help='Dimension for x-axis' />
        <param type="integer" name="dim_2" value='2' label="Y axis dimension" help='Dimension for y-axis' />
        <param type="data" name="cells_use" format="tabular" label="Cells list" help='File to be used to derive a vector of cells to plot (default is all cells)' optional='true'/>
        <param type="float" name="pt_size" value='1' label="Point size" help='Adjust point size for plotting' />
        <param type="float" name="label_size" value='4' label="Label size" help='Sets size of labels'/>
        <param type="boolean" name="do_label" checked="false" label='Label clusters' truevalue="TRUE" falsevalue="FALSE" />
        <param type="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways' />
        <param type="text" name="plot_title" format="text" label='Plot title' />
        <param type="boolean" name="do_bare" checked="false" label='Do only minimal formatting' truevalue="TRUE" falsevalue="FALSE" />
        <param type="text" name="cols_use" format="text" label="Colors" help='Comma-separated list of colors, each color corresponds to an identity class. By default, ggplot assigns colors.' />
        <param type="text" name="pt_shape" format="text" label="Cell attribute for shape" help='If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells.' />
        <param type="boolean" name="coord_fixed" checked="false" label="Fixed-scaled coordinate system" help='Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.' truevalue="TRUE" falsevalue="FALSE" />
        <param type="boolean" name="no_axes" checked="false" label="Remove Axes" help='Setting to TRUE will remove the axes.' truevalue="TRUE" falsevalue="FALSE" />
        <param type="boolean" name="dark_theme" checked="false" label='Use a dark theme for the plot..' truevalue="TRUE" falsevalue="FALSE" />
        <param type="text" name="plot_order" format="text" label="Ident (clusters) order" help='Comma-separated string specifying the order of plotting for the idents (clusters). This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top).' />
        <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.' />
        <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
    </inputs>
    <outputs>
        <data name="output_image_file" format="png" from_work_dir="pca.png" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="seurat_clustered.rds" />
            <output name="output_image_file" file="pca.png" />
        </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 graphs the output of a dimensional reduction technique (PCA by default). Cells are colored
by their identity class.

-----

**Inputs**

    * Seurat RDS object

-----

**Outputs**

    * PNG-format image file

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

@VERSION_HISTORY@

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