<tool id="signac_dimplot" name="Plot dimensional reduction" version="0.1.0" python_template_version="3.5">
<description> of your cell embeddings.</description>
<macros>
    <import>signac_macros.xml</import>
</macros>
<expand macro="requirements"/>
<stdio>
    <exit_code range="1:"/>
</stdio>
<command><![CDATA[
    Rscript '${__tool_directory__}'/signac-dimplot.R --signac-object $signac_object --dims $dims --pt-size $pt_size --label-size $label_size --group-by $group_by --png-width $png_width --png-height $png_height --output_image_file $dimplot_file
]]></command>
<inputs>
    <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
    <param type="text" name="dims" value='1,2' label="Dimensions to use." help='Dimension to use.'/>
    <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="text" name="group_by" value='ident' label='Group by' help='Group (color) cells in different ways'/>
    <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="dimplot_file" format="png" from_work_dir="Dimplot.png" label="Signac.dimplot.png"/>
</outputs>
<help><![CDATA[
This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
    ]]></help>
</tool>