<tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description></description>
    <macros>
        <import>bmcv.xml</import>
        <token name="@TOOL_VERSION@">0.2</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <creator>
        <expand macro="creators/bmcv" />
    </creator>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">galaxy_image_analysis</xref>
    </xrefs>
    <requirements> 
        <requirement type="package" version="0.14.2">scikit-image</requirement> 
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
        <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
        <requirement type="package" version="2.5.2">python-dateutil</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy
        ]]>
    </command>
    <inputs> 
        <param name="input" type="data" format="tabular" label="CSV point file"/> 
        <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" />
        <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" />
        <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> 
        <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" />
    </inputs>
    <outputs>
        <data name="output" format="tiff" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="points.tsv" />
            <param name="shapex" value="20" /> 
            <param name="shapey" value="30" />
            <param name="has_header" value="false" />
            <param name="invert_xy" value="true" />
            <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> 
        </test>
    </tests>
    <help>

        This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.

        The created image is a single-channel image with 16 bits per pixel (unsigned integer).
        The points are rasterized with value 32767 (white).
        Pixels not corresponding to any points in the CSV are assigned the value 0 (black).

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
    </citations>
</tool>