<tool id="seurat_dim_plot" name="Seurat Plot dimension reduction" version="@SEURAT_VERSION@_@VERSION@+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@
        #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>
        <expand macro="input_object_params"/>
        <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**

Graphs the output of a dimensional reduction technique on a 2D scatter plot
where each point is a cell and it's positioned based on the cell embeddings
determined by the reduction technique. By default, cells are colored by their
identity class (can be changed with the group.by parameter).

@SEURAT_INTRO@

-----

**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>