<tool id="pcdl_plot_scatter" name="pcdl_plot_scatter" version="3.0.1+galaxy0" profile="21.05">
    <macros>
        <import>pcdl_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement"/>
    </requirements>
    <command><![CDATA[
        #import re
        mkdir output_pc &&
        #for $file in $path:
            #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
            ln -s '$file' output_pc/$filename &&
        #end for

        pcdl_plot_scatter 'output_pc' '$focus_cell'
        --custom_data_type $custom_data_type
        --microenv $microenv
        --physiboss $physiboss
        --settingxml 'none'
        --verbose $verbose
        --z_slice $z_slice
        --z_axis '$z_axis'
        --alpha $alpha
        --cmap '$cmap'
        --title '$title'
        --grid $grid
        --legend_loc '$legend_loc'
        --xlim '$xlim'
        --ylim '$ylim'
        --xyequal $xyequal
        --s $s
        --figsizepx $figsizepx_x $figsizepx_y
        --directory 'jakku'
        --ext $ext
        --figbgcolor '$figbgcolor'
    ]]></command>
    <inputs>
        <section name="essential" title="essential:" expanded="true">
            <expand macro="path"/>
            <expand macro="focus_cell"/>
            <expand macro="custom_data_type"/>
            <expand macro="z_slice"/>
            <expand macro="z_axis"/>
            <expand macro="alpha"/>
            <expand macro="cmap"/>
            <expand macro="title"/>
            <expand macro="grid"/>
            <expand macro="legend_loc"/>
            <expand macro="xlim"/>
            <expand macro="ylim"/>
            <expand macro="xyequal"/>
            <expand macro="s"/>
            <expand macro="figsizepx_x"/>
            <expand macro="figsizepx_y"/>
            <expand macro="ext"/>
            <expand macro="figbgcolor"/>
        </section>
        <section name="advanced" title="advanced:" expanded="false">
            <expand macro="microenv"/>
            <expand macro="physiboss"/>
            <expand macro="verbose"/>
        </section>
    </inputs>
    <outputs>
        <collection name="scatter_plot" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;output.+)\.jpeg" format="jpg" directory="jakku" visible="false"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <section name="essential">
                <param name="path">
                    <expand macro="output"/>
                </param>
            </section>
            <section name="advanced">
                <param name="verbose" value="false"/>
            </section>
            <output_collection name="scatter_plot" count="2">
                <element name="output00000000_cell_type">
                    <assert_contents>
                        <has_text text="JFIF"/>
                    </assert_contents>
                </element>
                <element name="output00000001_cell_type">
                    <assert_contents>
                        <has_text text="JFIF"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Function generates pandas scatter plots.

Homepage: https://github.com/elmbeech/physicelldataloader
    ]]></help>
    <citations>
        <expand macro="citation"/>
    </citations>
</tool>